Viewing sorted genome BAM in IGV

[William Kath]

Hi,

I've been trying to view the genome sorted BAM file produced by RSEM (rsem-calculate-expression with option --output-genome-bam) using IGV.   I don't get any errors when loading the file, but no reads are displayed.   I have tried re-sorting with samtools, and changing IGV preferences to remove read filtering (by mapped quality, etc.).   Is there some additional step that I'm missing that must be done so that IGV recognizes RSEM's output?

"samtools view -c" reports plenty of reads, as does the genes.results file, and I'm looking at specific genes where non-zero TPM values are reported and at locations at which I can see reads when extracted with "samtools view".  

Thanks,

- Bill

[Bo Li]

Hi Bill,

Can you let me know which version of RSEM you have used?

Best,
Bo

> --
> RSEM website: http://deweylab.biostat.wisc.edu/rsem/ [1]
> ---
> You received this message because you are subscribed to the Google
> Groups "RSEM Users" group.
> To unsubscribe from this group and stop receiving emails from it,
> send an email to rsem-users+...@googlegroups.com.
> To post to this group, send email to rsem-...@googlegroups.com.
> Visit this group at https://groups.google.com/group/rsem-users [2].
>
>
> Links:
> ------
> [1] http://deweylab.biostat.wisc.edu/rsem/
> [2] https://groups.google.com/group/rsem-users

[William Kath]

Newly compiled from source:

$ rsem-calculate-expression --version

Current version: RSEM v1.2.31

IGV is the latest version, too: 2.3.78.   I run rsem-calculate-expression on a linux cluster and view reads on a macbook pro.

Thanks,

- Bill

[Bo Li]

Hi Bill,

Ah, that's the reason. In RSEM v1.2.31, you should turn on
--sort-bam-by-coordinate option to generated sorted genome bam and its
indices.

Hope it helps,
Bo

>>>  RSEM website: http://deweylab.biostat.wisc.edu/rsem/ [1] [1]

>>>  ---
>>>  You received this message because you are subscribed to the
>> Google
>>> Groups "RSEM Users" group.
>>>  To unsubscribe from this group and stop receiving emails from
>> it,
>>> send an email to rsem-users+...@googlegroups.com.
>>>  To post to this group, send email to rsem-...@googlegroups.com.
>>>  Visit this group at https://groups.google.com/group/rsem-users

>> [2] [2].
>>>
>>>
>>> Links:
>>> ------
>>> [1] http://deweylab.biostat.wisc.edu/rsem/ [1]
>>> [2] https://groups.google.com/group/rsem-users [2]

[William Kath]

I did.   The steps were:

STAR_2.5.2a --genomeDir [path to Gencode reference] --readFilesIn [long list of gzipped fastq files]  --readFilesCommand "gzip -cd" --outFileNamePrefix S13_ --runThreadN 20 --quantMode GeneCounts TranscriptomeSAM --outSAMtype BAM SortedByCoordinate

## calculate expression with rsem
rsem-calculate-expression -p 20 --bam --paired-end --forward-prob 0 --output-genome-bam --sort-bam-by-coordinate S13_Aligned.toTranscriptome.out.bam /projects/b1020/kath/rsem_1.2.31_Gencode22/rsem_1.2.31_Gencode22 S13_rsem_counts

I made the STAR and rsem indices with the *same* fasta and gtf reference, Gencode 22.   I can view the STAR-aligned and sorted reads in IGV (using reference hg38), but not the ones output by rsem.

FYI, the libraries were made with the Illumina Truseq stranded kit.   The counts seem OK.

Thanks,

- Bill

[Bo Li]

Hi Bill,

Why not use RSEM's default STAR parameters? In particular, you should
not sort STAR-generated BAM by coordinates. This will break RSEM's
requirement that all alignments of a same read are grouped together.

Hope it helps,
Bo

>>>>> [1] http://deweylab.biostat.wisc.edu/rsem/ [1] [1]
>>>>> [2] https://groups.google.com/group/rsem-users [2] [2]

[William Kath]

I will certainly try letting rsem call STAR.   But note I'm asking STAR to both produce an "Aligned.sortedByCoord" BAM and an "Aligned.toTranscriptome" BAM.   The first is sorted by coordinate, but (I believe) the transcriptome alignment has the read pairs grouped together.   Here's a few reads from the latter:

[kath@quser13 S13]$ samtools view S13_Aligned.toTranscriptome.out.bam | head -8
K00242:78:HF2NWBBXX:2:1101:27316:21887    163    ENST00000387347.2    907    255    100M    =    992    185    CCCTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAATTAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGA    <-A7FAFJFFA-F<JJA7FFFFAFJFF<<F7FJJAA<<<-F<AFA<<AJ7--F7<-7A-77-7777-777777FJ7A<7F<--77F<JJ-A-7FF7--7-    NH:i:1    HI:i:1
K00242:78:HF2NWBBXX:2:1101:27316:21887    83    ENST00000387347.2    992    255    100M    =    907    -185    ACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAGTAC    FAFA-JJJJA<JJJAJJAJF77AAA7<AJJJFJA<<FJA7F<<FJFA<FAJFJJA-AF-AJ<AJAJAFFJJFJAAJJJ<F<FJFJJAJFJFJJJFFFFA-    NH:i:1    HI:i:1
K00242:78:HF2NWBBXX:2:1101:27478:21887    163    ENST00000490232.3    177    255    100M    =    182    105    GGGGTGAACCGGCCCAGGTCGGAAACGGAGCAGGTCAAAACTCCCGTGCTGATCAGTAGTGGGATCGCGCCTGTGAATAGCCACTGCACTCCAGCCTGAG    AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ    NH:i:1    HI:i:1
K00242:78:HF2NWBBXX:2:1101:27478:21887    83    ENST00000490232.3    182    255    100M    =    177    -105    GAACCGGCCCAGGTCGGAAACGGAGCAGGTCAAAACTCCCGTGCTGATCAGTAGTGGGATCGCGCCTGTGAATAGCCACTGCACTCCAGCCTGAGCAACA    JFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA    NH:i:1    HI:i:1
K00242:78:HF2NWBBXX:2:1101:27559:21887    163    ENST00000387347.2    218    255    100M    =    289    171    GCCAAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAG    AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ7FJJFJJJJFJFJFJJFJJJJJJJAJJFJJJJJJJJJ    NH:i:1    HI:i:1
K00242:78:HF2NWBBXX:2:1101:27559:21887    83    ENST00000387347.2    289    255    100M    =    218    -171    CAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTAAATTTGCC    JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA    NH:i:1    HI:i:1
K00242:78:HF2NWBBXX:2:1101:28716:21887    163    ENST00000490232.3    10    3    100M    =    78    168    GGTGGCGCGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGGGTG    AAAFFJJJJJFJJJJJJFJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJFJJJJJJ    NH:i:2    HI:i:1
K00242:78:HF2NWBBXX:2:1101:28716:21887    83    ENST00000490232.3    78    3    100M    =    10    -168    TCTGGGCTGTAGTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCATCAATATGGTGACCTCCCGGGAGCGGGGGACCACCAGGTTGCCTAAGGAG    JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA    NH:i:2    HI:i:1

Does rsem need more sorting than this (e.g., all reads on the transcript together)?

Another thing I noticed.   STAR sorts genomic reads in this chromosome order (viewed with samtools -H)

@SQ    SN:chr1    LN:248956422
@SQ    SN:chr2    LN:242193529
@SQ    SN:chr3    LN:198295559
@SQ    SN:chr4    LN:190214555
@SQ    SN:chr5    LN:181538259
@SQ    SN:chr6    LN:170805979
@SQ    SN:chr7    LN:159345973
@SQ    SN:chr8    LN:145138636
@SQ    SN:chr9    LN:138394717
@SQ    SN:chr10    LN:133797422
@SQ    SN:chr11    LN:135086622
@SQ    SN:chr12    LN:133275309
@SQ    SN:chr13    LN:114364328
@SQ    SN:chr14    LN:107043718
@SQ    SN:chr15    LN:101991189
@SQ    SN:chr16    LN:90338345
@SQ    SN:chr17    LN:83257441
@SQ    SN:chr18    LN:80373285
@SQ    SN:chr19    LN:58617616
@SQ    SN:chr20    LN:64444167
@SQ    SN:chr21    LN:46709983
@SQ    SN:chr22    LN:50818468
@SQ    SN:chrX    LN:156040895
@SQ    SN:chrY    LN:57227415
@SQ    SN:chrM    LN:16569

which matches the order in the reference genome, but the rsem-sorted order is:

@SQ    SN:chr1    LN:248956422
@SQ    SN:chr10    LN:133797422
@SQ    SN:chr11    LN:135086622
@SQ    SN:chr12    LN:133275309
@SQ    SN:chr13    LN:114364328
@SQ    SN:chr14    LN:107043718
@SQ    SN:chr15    LN:101991189
@SQ    SN:chr16    LN:90338345
@SQ    SN:chr17    LN:83257441
@SQ    SN:chr18    LN:80373285
@SQ    SN:chr19    LN:58617616
@SQ    SN:chr2    LN:242193529
@SQ    SN:chr20    LN:64444167
@SQ    SN:chr21    LN:46709983
@SQ    SN:chr22    LN:50818468
@SQ    SN:chr3    LN:198295559
@SQ    SN:chr4    LN:190214555
@SQ    SN:chr5    LN:181538259
@SQ    SN:chr6    LN:170805979
@SQ    SN:chr7    LN:159345973
@SQ    SN:chr8    LN:145138636
@SQ    SN:chr9    LN:138394717
@SQ    SN:chrM    LN:16569
@SQ    SN:chrX    LN:156040895
@SQ    SN:chrY    LN:57227415

I tried rearranging the chromosome order in the header and resorting, but this didn't seem to help.

Thanks,

- Bill

[Bo Li]

Hi Bill,

Can you send me a minimal set of BAM files to repeat this issue? I'll
look into it.

Best,
Bo

>>>>>>> [1] http://deweylab.biostat.wisc.edu/rsem/ [1] [1] [1]
>>>>>>> [2] https://groups.google.com/group/rsem-users [2] [2] [2]

[William L. Kath]

Hi Bo,

Here's an update:

1. I tried several times pulling out the alignments falling on a few genes and converting them back to fastq.   When these were run through the pipeline, however, there was no problem with viewing them.
   
   
2. I tried letting rsem call STAR for aligning, as you specified.   Again, no problem.
   
   
3. Not knowing what else to do, I tried using IGV on the cluster where the alignments were done, viewing with XWindows.   It's *really slow*, but when IGV is started from a shell there's a running dialog in the terminal giving useful information, and I thought I might see something that could give a hint about the problem.   Surprisingly, however, the alignments could be viewed fine!
   
   
4. I tried re-transferring the 18 GB BAM file to the research share I mount on my mac to view the alignments.   Surprise, surprise, this time there wasn't any problem.
   

So, I'm not sure what was corrupt in the file, but it looks like this was the problem.   There was trouble in the past just after this particular storage device was installed when the load was high (i.e., lots of people doing high-speed transfers).   I thought that issue had been dealt with (at least, I haven't had trouble of this type in a long while), and when it had happened in the past there were clear timeout errors messages.

So, my apologies, it wasn't a problem with rsem at all.  

Thanks very much,

- Bill

with

 RSEM website: https://urldefense.proofpoint.com/v2/url?u=http-3A__deweylab.biostat.wisc.edu_rsem_&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=txU0koP1iYAU5qC-w8p2J4K7HW2Czqk8DgwOjEvvnVQ&e=  [1] [1]

[1]

[1]

 ---
 You received this message because you are subscribed to the

Google

Groups "RSEM Users" group.
 To unsubscribe from this group and stop receiving emails

from

it,

send an email to rsem-users+...@googlegroups.com.
 To post to this group, send email to

rsem-...@googlegroups.com.

 Visit this group at

https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&e=  [2]

[2]

[2] [2].

Links:
------
[1] https://urldefense.proofpoint.com/v2/url?u=http-3A__deweylab.biostat.wisc.edu_rsem_&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=txU0koP1iYAU5qC-w8p2J4K7HW2Czqk8DgwOjEvvnVQ&e=  [1] [1] [1]
[2] https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&e=  [2] [2] [2]

 --
 RSEM website: https://urldefense.proofpoint.com/v2/url?u=http-3A__deweylab.biostat.wisc.edu_rsem_&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=txU0koP1iYAU5qC-w8p2J4K7HW2Czqk8DgwOjEvvnVQ&e=  [1] [1]

[1]

 ---
 You received this message because you are subscribed to the

Google

Groups "RSEM Users" group.
 To unsubscribe from this group and stop receiving emails from

it,

send an email to rsem-users+...@googlegroups.com.
 To post to this group, send email to

rsem-...@googlegroups.com.

 Visit this group at https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&e=

[2]

[2] [2].

Links:
------
[1] https://urldefense.proofpoint.com/v2/url?u=http-3A__deweylab.biostat.wisc.edu_rsem_&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=txU0koP1iYAU5qC-w8p2J4K7HW2Czqk8DgwOjEvvnVQ&e=  [1] [1]
[2] https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&e=  [2] [2]

 --
 RSEM website: https://urldefense.proofpoint.com/v2/url?u=http-3A__deweylab.biostat.wisc.edu_rsem_&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=txU0koP1iYAU5qC-w8p2J4K7HW2Czqk8DgwOjEvvnVQ&e=  [1] [1]

 ---
 You received this message because you are subscribed to the

Google

Groups "RSEM Users" group.
 To unsubscribe from this group and stop receiving emails from

it,

send an email to rsem-users+...@googlegroups.com.
 To post to this group, send email to rsem-...@googlegroups.com.

 Visit this group at https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&e=

[2] [2].

Links:
------
[1] https://urldefense.proofpoint.com/v2/url?u=http-3A__deweylab.biostat.wisc.edu_rsem_&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=txU0koP1iYAU5qC-w8p2J4K7HW2Czqk8DgwOjEvvnVQ&e=  [1]
[2] https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&e=  [2]

 --
 RSEM website: https://urldefense.proofpoint.com/v2/url?u=http-3A__deweylab.biostat.wisc.edu_rsem_&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=txU0koP1iYAU5qC-w8p2J4K7HW2Czqk8DgwOjEvvnVQ&e=  [1]

 ---
 You received this message because you are subscribed to the Google
Groups "RSEM Users" group.
 To unsubscribe from this group and stop receiving emails from it,
send an email to rsem-users+...@googlegroups.com.
 To post to this group, send email to rsem-...@googlegroups.com.

 Visit this group at https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&e=  [2].


Links:
------
[1] https://urldefense.proofpoint.com/v2/url?u=http-3A__deweylab.biostat.wisc.edu_rsem_&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=txU0koP1iYAU5qC-w8p2J4K7HW2Czqk8DgwOjEvvnVQ&e= [2] https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&e=

-- 
William L. Kath, Professor
Engineering Sciences and Applied Mathematics
McCormick School of Engineering, Northwestern University
2145 Sheridan Road, Evanston, IL 60208-3125
Phone: 847-491-8784   Fax: 847-491-2178

[Bo Li]

Hi Bill,

Glad to hear you find out what happened :)

Best,
Bo

On 2016-07-05 09:26, William L. Kath wrote:
> Hi Bo,
>
> Here's an update:
>

> * I tried several times pulling out the alignments falling on a few

> genes and converting them back to fastq.   When these were run
> through the pipeline, however, there was no problem with viewing them.
>
>

> * I tried letting rsem call STAR for aligning, as you specified.  
> Again, no problem.
>
> * Not knowing what else to do, I tried using IGV on the cluster where

> the alignments were done, viewing with XWindows.   It's *really
> slow*, but when IGV is started from a shell there's a running dialog
> in the terminal giving useful information, and I thought I might see
> something that could give a hint about the problem.   Surprisingly,
> however, the alignments could be viewed fine!
>

> * I tried re-transferring the 18 GB BAM file to the research share I

>> [1]  [1] [1] [1]
>> [2]
>>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&d=CwIFaQ&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&e=
>> [2]  [2] [2] [2]

> William L. Kath, Professor
> Engineering Sciences and Applied Mathematics
> McCormick School of Engineering, Northwestern University
> 2145 Sheridan Road, Evanston, IL 60208-3125
> Phone: 847-491-8784 Fax: 847-491-2178
>

> --
> RSEM website: http://deweylab.biostat.wisc.edu/rsem/ [3]

> ---
> You received this message because you are subscribed to the Google
> Groups "RSEM Users" group.
> To unsubscribe from this group and stop receiving emails from it,
> send an email to rsem-users+...@googlegroups.com.
> To post to this group, send email to rsem-...@googlegroups.com.

> Visit this group at https://groups.google.com/group/rsem-users [4].
>
>
> Links:
> ------
> [1]
> https://urldefense.proofpoint.com/v2/url?u=http-3A__deweylab.biostat.wisc.edu_rsem_&amp;d=CwIFaQ&amp;c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&amp;r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&amp;m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&amp;s=txU0koP1iYAU5qC-w8p2J4K7HW2Czqk8DgwOjEvvnVQ&amp;e=
> [2]
> https://urldefense.proofpoint.com/v2/url?u=https-3A__groups.google.com_group_rsem-2Dusers&amp;d=CwIFaQ&amp;c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&amp;r=Xm-H2K5ZnbjBC6dphv-weRxsDm4H1MAXpJnPiMySh9o&amp;m=Fdm7h2lseS-RkBwWwhl4VraTsKHorn9xJJIZAVF_cnI&amp;s=i9i-O5X65oatppFz7eAJ8NGY0uOdb8Ofpv_ZJUztu9o&amp;e=
> [3] http://deweylab.biostat.wisc.edu/rsem/
> [4] https://groups.google.com/group/rsem-users