feature counts script output help please help

Question

[smithkthedale]

Where are my feature count files going when I use this script:

featureCounts -a ncbi_dataset/data/GCA_002738495.1/genomic.gff \
-o Feature_counts.txt \
-p -s 2 -T 10 \
*_sorted.bam

It's running but can't find the file...no feature_counts.txt folder or cd?

RNAseq_CD_1_CCGCGGTT_Arabidopsis_I1187_L1_sorted.bam

Are they in these folders? I thought these folders were just the sam to bam conversion ones.

[smithkthedale]

what should the new files end in? .featurecounts?

[rpolicastro]

I think featureCounts prints a log to standard output, which if you provide to use can help us figure out the problem.

[smithkthedale]

how do I use verbose in my script. when I type in verbose it says command not found

[Mensur Dlakic]

It says so already right below your question:

Maybe add the --verbose switch to your command and tell us what was the screen output.

That means adding --verbose to your featureCounts command anywhere before you type *_sorted.bam.

Answer 1

[Mensur Dlakic]

If you type featureCounts without any arguments, it will give help:

  -o <string>         Name of output file including read counts. A separate file
                      including summary statistics of counting results is also
                      included in the output ('<string>.summary'). Both files
                      are in tab delimited format.

Based on your commands, it should be saved in Feature_counts.txt. Maybe add the --verbose switch to your command and tell us what was the screen output.