featurecounts in command line
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6 weeks ago
gina02 ▴ 50

I'm trying to convert my bam files to count data with the help of feature counts in command line, I used the code:

featurecounts -T 8 -a /Users/ria/Desktop/bowtie_2/GCF_000001405.39_GRCh38.p13_genomic.gtf -g 'transcrip_id' -o readcounts/readcount1.txt bam files/-.bam   

(readcounts is a the directory for dumping the output)

the error im getting is:ERROR: temporary directory is not writable: 'readcounts'

what does that mean?

data rna count seq bam files • 216 views
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Hi,

Does the folder readcounts exist? If so, can you write into it? (can you create a text file under that folder?)

If so, perhaps featureCounts does not accept a path file name, but only file name, although I think it does.

Test if you can create a file under the directory readcounts (assuming that this folder exists), which you can do in linux by (otherwise create it by saving a dummy text file under this folder):

touch readcounts/fake_empty_file.txt

Check if it was created, if it was, try to run the program without giving the folder.

I hope this helps,

António

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Entering edit mode

Problem may be with this

bam files/-.bam 

Is that a directory with a space in the name bam files? That is bad practice. Also -.bam is not how you include all BAM files. Wild card use would be *.bam. You may need to escape the space so try bam\ files/*.bam or ideally change the name of directory and do bam_files/*.bam.

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