How to solve this featureCounts problem ?

Question

[AIMAR]

Hello everyone, I hope you're all doing well! I'm seeking assistance with FeatureCounts for my RNA-seq analysis. I'm using a for loop to process my samples, but I encounter this error with FeatureCounts:

ERROR: temporary directory is not writable: '/home/inda/motorola/RNASeq/Results_RNA_seq/Alignment/Feat_Counts/SRR33194007'

However, when I run the FeatureCounts command for a single sample (without the loop), it works fine. I've attempted to resolve this by adjusting permissions with a command, but the issue persists. Can anyone help?

[GenoMax]

I'm using a for loop to process my samples, but I encounter this error with FeatureCounts:

ERROR: temporary directory is not writable:

Consider specifying unique output directories at the level of $SAMPLE. My guess is the process that makes the original directory locks it so other processes using that name can't write to it (especially if your for loop is starting multiple processes at the same time).

Use *.bam as input for relevant files as ATpoint suggests. You will get a column of counts for each bam in one count matrix.

[AIMAR]

Thank you very much I'll try it.

Answer 1

[AIMAR]

I've tried with the *.bam and it's worked. Thanks very much!

Answer 2

[ATpoint]

Please limit code examples to relevant sections only. All this messaging distracts. Also, please use copy-paste and the markdown highlighting option (the 10101 button) and not screenshots. Do you need all this chmoding? A normal disk should be writable for standard users, no? Not sure who is the owner of the tmp files from featureCounts. Also, featureCounts can process many bams at once, there is no need to loop over every file. Just use *.bam as argument for the bam files.

[AIMAR]

I've tried to use the code section buttom but didn't work. And each BAM file is placed on it's own repository so I don't know how to set featureCounts to find all concerning BAM file. So if you've a idea how I can resolve this problem then I can move on the analysis it'll be helpfull

Thanks

[GenoMax]

I've tried to use the code section buttom but didn't work.

Have you seen --> How to Use Biostars Part-3: Formatting Text and Using GitHub Gists

[AIMAR]

Yes, but I didn't remember the name Gist but It was clear that I can use something called Github .... to share my code in my post.

[GenoMax]

You do not need to use GitHub gist (unless you are trying to share a large amount of code). You can simply copy paste the text that you want to show as code and then highlight the text by selecting it in edit window. Then click on 101010 button to format as code. Voila!