Running STAR without a .gtf annotation

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Joseph Mudd

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Nov 7, 2016, 2:22:43 PM11/7/16
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Hello all,

I am trying to determine the percentage of reads in my sample mapping to ribosomal rRNA sequences.  Unfortunately the Rhesus macaque .gtf I am using is not annotating for rRNAs or other small non-coding RNAs.  To get around this, I indexed a small .fasta file I compiled containing 18S rRNA sequences from rhesus macaques.  For this particular run, I did not include an annotation file.  I am simply interested in reads mapping to my small .fasta reference.  When I try to align to the indexed .fasta:

###
/hpcdata/lmm/lmm_data/muddjc/STAR-2.5.2b/bin/Linux_x86_64/STAR --genomeDir /hpcdata/lmm/lmm_data/muddjc/18S_index --readFilesIn <.fastq> --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 --outFilterMismatchNmax 2 --outFileNamePrefix /hpcdata/lmm/lmm_data/muddjc/JB37_18S_test
Nov 02 15:19:23 ..... started STAR run
Nov 02 15:19:23 ..... loading genome

Transcriptome.cpp:51:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /hpcdata/lmm/lmm_data/muddjc/18S_index/exonGeTrInfo.tab
Solution: check that the file exists and you have read permission for this file
SOLUTION: utilize --sjdbGTFfile /path/to/annotantions.gtf option at the genome generation step or mapping step

Nov 02 15:19:24 ...... FATAL ERROR, exiting
###

It seems that STAR is wanting an annotation file for the alignment.  I think because no gtf is provided in the index step, it's not generating the "exonGeTrinfo.tab".  Is it possible to run the alignment without a .gtf and how might I modify my command to accomplish this?

Thanks so much.

jc


Alexander Dobin

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Nov 8, 2016, 6:40:40 PM11/8/16
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Hi Joseph,

if you do not have annotations, you cannot use the --quantMode GeneCounts option.

Cheers
Alex

nikolay....@scilifelab.se

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Apr 16, 2018, 10:15:05 AM4/16/18
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Hi Alex,

I also problem running star without gtf. I tried to aligned 1 PE read to hg38 human genome prepared in two different ways: 1) genome generate with --sjdbGTFfile, 2) genome generate without --sjdbGTFfile. In the case 1) it took 1 second to run star alignment and I got a BAM file. In the case 2) star reached step "Started mapping" and never finished, I see that it run with "top" command and I waited for many hours. So something is wrong here. My command line was:

star --genomeDir hg38_generate_without_gtf --readFilesIn test1.fastq test2.fastq --outFilterMismatchNmax 5 --runThreadN 8 --outReadsUnmapped Fastx --outFileNamePrefix test --outSAMtype BAM SortedByCoordinate --sjdbOverhang 149

Could you let me know what can be wromg here? Thanks!

Best,
Nikolay

Alexander Dobin

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Apr 16, 2018, 6:08:40 PM4/16/18
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Hi Nikolay,

please try to map it without --sjdbOverhang 149, and if it does not work, send me the Log.out file.

Cheers
Alex
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