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RSeQC FAQ list !
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Asmita Shrestha
8/29/24
Issue with bed file for read_distribution.py
Hi, I need bed file of sus scrofa appropriate for read_distribution.py. I tried making with gtf file
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Issue with bed file for read_distribution.py
Hi, I need bed file of sus scrofa appropriate for read_distribution.py. I tried making with gtf file
8/29/24
Kokulapalan Wimalanathan
,
SCP- 049
2
10/23/22
junction_annotation.py bed12 file
You can consider the score as “number of reads” if one read only split once. But keep in mind long
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junction_annotation.py bed12 file
You can consider the score as “number of reads” if one read only split once. But keep in mind long
10/23/22
radhika iyer
9/1/22
Mouse refseq bed file on RseQc website
Hi, I see that mouse bed file to be used as input for RseQc tool is available for download on your
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Mouse refseq bed file on RseQc website
Hi, I see that mouse bed file to be used as input for RseQc tool is available for download on your
9/1/22
Yue Zhao
, …
payal banerjee
5
6/22/22
How to generate ribosome BED file
Thank you very much. This bed file works. Please post it on RSeQC website. I am sure many will
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How to generate ribosome BED file
Thank you very much. This bed file works. Please post it on RSeQC website. I am sure many will
6/22/22
payal banerjee
6/21/22
mm39 rRNA bed file
Hello, Please direct how to download rRNA bed file for mm39 from UCSC genome browser. They don't
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mm39 rRNA bed file
Hello, Please direct how to download rRNA bed file for mm39 from UCSC genome browser. They don't
6/21/22
Liguo Wang
1/27/21
Re: mismatch_profile
Hi Philipp, It only has two filters: read_number and MAPQ. I check the code (v4.0.0), it looks OK.
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Re: mismatch_profile
Hi Philipp, It only has two filters: read_number and MAPQ. I check the code (v4.0.0), it looks OK.
1/27/21
magnus jespersen
,
Liguo Wang
5
8/3/20
Information needed in .bed file for geneBody_coverage.py
Standard BED file has 12 fields. The first 6 fields define the transcribed region. The last 6 fields
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Information needed in .bed file for geneBody_coverage.py
Standard BED file has 12 fields. The first 6 fields define the transcribed region. The last 6 fields
8/3/20
Vempalli Fazulur
,
Joshua Wang
3
4/30/20
RSeQC read_distribution zero tag counts for Zebrafish RNASeq data
Dear Liguo, Thanks a lot. bed file chromosomes are not consistent with bam. After I remove 'chr
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RSeQC read_distribution zero tag counts for Zebrafish RNASeq data
Dear Liguo, Thanks a lot. bed file chromosomes are not consistent with bam. After I remove 'chr
4/30/20
hcb...@ucsc.edu
11/27/18
hg38_GENCODE_v23.bed MD5
Hi-- I see that hg38_GENCODE_v23.bed.gz isn't on sourceforge any more. I have a copy locally, but
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hg38_GENCODE_v23.bed MD5
Hi-- I see that hg38_GENCODE_v23.bed.gz isn't on sourceforge any more. I have a copy locally, but
11/27/18
Jon
,
Liguo Wang
3
6/21/18
Cannot get coverage signal from bam
Hi Liguo, Thank you for your prompt reply, I tried to look into my BAM file (which I have converted
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Cannot get coverage signal from bam
Hi Liguo, Thank you for your prompt reply, I tried to look into my BAM file (which I have converted
6/21/18
Gonzalo S. Nido
,
Liguo Wang
3
2/7/18
Median TIN is anticorrelated with RIN
First of all, thank you for your prompt response. The data I'm analyzing is ribo-depleted RNA-seq
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Median TIN is anticorrelated with RIN
First of all, thank you for your prompt response. The data I'm analyzing is ribo-depleted RNA-seq
2/7/18
Nikelle Petrillo
,
Liguo Wang
4
11/9/17
Understanding read_distribution.py output
Sorry for late reply. It's probably because 3' and 5' UTR were not defined in you BED
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Understanding read_distribution.py output
Sorry for late reply. It's probably because 3' and 5' UTR were not defined in you BED
11/9/17
MNoon
,
Liguo Wang
2
10/30/17
doesn't pickup qcmodule which is on the path
Hi, you need to setup PYTHONPATH not PATH, for example: export PYTHONPATH==/unsupported/nirav/RSeQC/
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doesn't pickup qcmodule which is on the path
Hi, you need to setup PYTHONPATH not PATH, for example: export PYTHONPATH==/unsupported/nirav/RSeQC/
10/30/17
Tiffany L
, …
bioinformati...@gmail.com
4
9/7/17
question about infer_experiment.py
Hi Cara Make sure that the chromosome names in BED file and SAM file have the same name they should
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question about infer_experiment.py
Hi Cara Make sure that the chromosome names in BED file and SAM file have the same name they should
9/7/17
mehr...@broadinstitute.org
,
Liguo Wang
3
8/15/17
junction_saturation.py resampling
Thank you for confirming this! On Tuesday, August 15, 2017 at 10:32:56 AM UTC-4, Liguo Wang wrote:
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junction_saturation.py resampling
Thank you for confirming this! On Tuesday, August 15, 2017 at 10:32:56 AM UTC-4, Liguo Wang wrote:
8/15/17
mehr...@broadinstitute.org
,
Liguo Wang
9
7/26/17
gtf2bed issue
That is true, the coordinate is Base1 vs Base 0. Thank you ! On Tuesday, July 25, 2017 at 3:55:42 PM
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gtf2bed issue
That is true, the coordinate is Base1 vs Base 0. Thank you ! On Tuesday, July 25, 2017 at 3:55:42 PM
7/26/17
Ido Tamir
, …
john.al...@sheffield.ac.uk
6
5/4/17
total tags vs assigned tags read_distribution.py
Hiya, I've run into the same problem. Total Reads 53536146 Total Tags 69334788 Total Assigned
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total tags vs assigned tags read_distribution.py
Hiya, I've run into the same problem. Total Reads 53536146 Total Tags 69334788 Total Assigned
5/4/17
Michael zhou
, …
Indugu Nagaraju
6
6/3/16
junction_saturation.py error -- ValueError: tid -1 out of range 0<=tid<25
Hi I am getting same error meassage when I run junction_saturation.py. Michael how you solved this
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junction_saturation.py error -- ValueError: tid -1 out of range 0<=tid<25
Hi I am getting same error meassage when I run junction_saturation.py. Michael how you solved this
6/3/16
baptiste mossotti
,
Liguo Wang
3
3/21/16
Problem with the BED file, junction_annotation
Hi Liguo, Thank you for your reply. I just resolved my problem. The file that I downloaded is the
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Problem with the BED file, junction_annotation
Hi Liguo, Thank you for your reply. I just resolved my problem. The file that I downloaded is the
3/21/16
rspreafico
,
Liguo Wang
2
6/22/15
Error with bam2wig.py
Hi Roberto, Thanks for identifying this bug. Yes, your fix is perfect. We will update the code. Liguo
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Error with bam2wig.py
Hi Roberto, Thanks for identifying this bug. Yes, your fix is perfect. We will update the code. Liguo
6/22/15
Darius Khan
,
Liguo Wang
3
6/15/15
geneBody_coverage.py - calculation details and interpreting the output
How exactly is this normalization carried out? See attachment. How should the Y-axis of the output
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geneBody_coverage.py - calculation details and interpreting the output
How exactly is this normalization carried out? See attachment. How should the Y-axis of the output
6/15/15
long le
,
Liguo Wang
4
3/30/15
DNA vs RNA quality control
We just checked the results of junction_annotation.py and also bam_stat.py. It seems that RSeqC is
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DNA vs RNA quality control
We just checked the results of junction_annotation.py and also bam_stat.py. It seems that RSeqC is
3/30/15
long le
3/25/15
RSeqC and bwa-mem
We have targeted RNA-Seq data mapped with the latest bwa-mem. How does RSeqC treat chimeric
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RSeqC and bwa-mem
We have targeted RNA-Seq data mapped with the latest bwa-mem. How does RSeqC treat chimeric
3/25/15
Gy. A
,
Liguo Wang
2
2/23/15
No output and no visualization with
read_distribution.py will output some thing like this: Group Total_bases Tag_count Tags/Kb CDS_Exons
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No output and no visualization with
read_distribution.py will output some thing like this: Group Total_bases Tag_count Tags/Kb CDS_Exons
2/23/15
Liguo Wang
8/27/14
Update: visualize gene body coverage of multiple RNA-seq samples
RSeQC v2.4 update: Rewrite “geneBody_coverage.py” 1) Memory-efficient: RAM consumption < 100M 2)
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Update: visualize gene body coverage of multiple RNA-seq samples
RSeQC v2.4 update: Rewrite “geneBody_coverage.py” 1) Memory-efficient: RAM consumption < 100M 2)
8/27/14
Yuan Hao
,
Liguo Wang
3
8/15/14
bam_stat.py error
Hi there, Thanks a million for the info. Problem resolved! Cheers, Yuan On Friday, August 15, 2014 10
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bam_stat.py error
Hi there, Thanks a million for the info. Problem resolved! Cheers, Yuan On Friday, August 15, 2014 10
8/15/14
Dejian
,
Liguo Wang
3
6/30/14
weird gene body coverage
Hi Liguo, Thanks for your quick response. Your first explanation is right. I checked the bam file,
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weird gene body coverage
Hi Liguo, Thanks for your quick response. Your first explanation is right. I checked the bam file,
6/30/14
Xueqiu Lin
,
Liguo Wang
6
6/23/14
BSeQC_RPKM
If concatenation of the first 6 columns (chrom, start, end, name, score, strand) of each bed entry
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BSeQC_RPKM
If concatenation of the first 6 columns (chrom, start, end, name, score, strand) of each bed entry
6/23/14
Michael zhou
,
Liguo Wang
2
5/6/14
how can i output the result of bam_stat.py to a text file? thx
The output was directed to STDERR, so you can use 2> to redirect to file. eg: bam_stat.py 2>
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how can i output the result of bam_stat.py to a text file? thx
The output was directed to STDERR, so you can use 2> to redirect to file. eg: bam_stat.py 2>
5/6/14
ASHWINI YADAV
,
Liguo Wang
10
4/30/14
no out put in output.clipping_profile.r
The polyA selection protocol has a little bit 3' bias. The coverage was also affected by your RNA
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no out put in output.clipping_profile.r
The polyA selection protocol has a little bit 3' bias. The coverage was also affected by your RNA
4/30/14
