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MonashBioinformaticsPlatform / RSeQC

fork of RSeQC python RNAseq metrics suit of tools
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geneBody_coverage.py no output #8

Open jingydz opened 2 years ago

jingydz commented 2 years ago

command

geneBody_coverage.py -r /xxx/mm10/mm10_RefSeq.bed -i xxx_cutadapt.bam -o geneBody_coverage_output

log

@ 2022-08-22 00:58:30: Read BED file (reference gene model) ... @ 2022-08-22 00:58:46: Total 106520 transcripts loaded @ 2022-08-22 00:58:46: Get BAM file(s) ... Sample Skewness @ 2022-08-22 00:58:46: Running R script ... null device 1

After I run the command, I got three files: geneBody_coverage_output.geneBodyCoverage.txt, geneBody_coverage_output.geneBodyCoverage.r, geneBody_coverage_output.geneBodyCoverage.curves.pdf

$cat geneBody_coverage_output.geneBodyCoverage.r pdf("geneBody_coverage_output.geneBodyCoverage.curves.pdf") x=1:100 icolor = colorRampPalette(c("#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"))(0) dev.off()

$cat geneBody_coverage_output.geneBodyCoverage.txt Percentile 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100

But I can't open the pdf file ( broken )

hclhcl123456 commented 2 years ago

Hello, I also have such a problem. Have you solved it now？

tomitomitom commented 2 years ago

Hi,

You need to index your bam (generation of a bai file) before using geneBody_coverage.py.

Run : samtools sort -m 1000000000 xxx_cutadapt.bam xxx_cutadapt.bam samtools index xxx_cutadapt.bam

and need you can run:

geneBody_coverage.py -r /xxx/mm10/mm10_RefSeq.bed -i xxx_cutadapt.bam -o geneBody_coverage_output

ttttuck commented 1 year ago

Hello everyone.

I'm getting no output, it's yielding the same error as @jingydz.

I use samtools to index my STAR sortedByCoordinate bam file.

samtools index SRR143_Aligned.sortedByCoord.out.bam SRR143_Aligned.sortedByCoord.out.bam.bai

And then, I run

geneBody_coverage.py -r gencode.v41.RefSeq.bed -i SRR143_Aligned.sortedByCoord.out.bam.bai -o SRR143gbc

But it wont work. Any help, please?

Thanks

zhongshuai666 commented 11 months ago

Hello everyone.

I'm getting no output, it's yielding the same error as @jingydz.

I use samtools to index my STAR sortedByCoordinate bam file.

samtools index SRR143_Aligned.sortedByCoord.out.bam SRR143_Aligned.sortedByCoord.out.bam.bai

And then, I run

geneBody_coverage.py -r gencode.v41.RefSeq.bed -i SRR143_Aligned.sortedByCoord.out.bam.bai -o SRR143gbc

But it wont work. Any help, please?

Thanks

you should use bam instead of bai geneBody_coverage.py -r gencode.v41.RefSeq.bed -i SRR143_Aligned.sortedByCoord.out.bam -o SRR143gbc

AzureLii commented 10 months ago

Hello, I also encountered the same situation, the main reason is that the bam and bam.bai files in my input folder are linked using "ln -s", and then the problem is solved by directly using the source file.

sparthib commented 9 months ago

HI @AzureLii, I have the same problem. Could you explain what you mean by directly using the source file? Thanks!

AzureLii commented 4 months ago

HI @AzureLii, I have the same problem. Could you explain what you mean by directly using the source file? Thanks!

oh, my God, I'm sorry I didn't see it until now. I made a mistake. The source file refers to the original file, that is, the result file (xxx.bam) and index file (.bai) are directly used instead of the ln-S link file. It just seems from your description that the problems we encountered should be different, so the answer should have no reference value for you.