Problem when running FeatureCounts

Question

[luzglongoria]

Hi! I have run STAR for mapping my reads with my reference genome. I got a BAM file and now I want to run FeatureCounts in my server. However, despite I have read the manual it seems to be a problem with the input argument:

featureCounts -a /path/to/genome_reference/GCF_000209185.1_CulPip1.0_genomic.gff -o Table.count input_file1 Aligned_mosquito.out.bam 

ERROR: invalid parameter: 'input_file1'

I have "only" one BAM file since the mapping was carried out with the --readFileManifest in STAR:

STAR --runThreadN 20 --genomeDir /path/to/folder/ --readFilesManifest /path/to/file/with/sample_names/samples.txt

this .txt file looks like: (tab separated)

bm-R1_1.fp.fq.gz        bm-R1_2.rp.fq.gz        bm
bm-R2_1.fp.fq.gz        bm-R2_2.rp.fq.gz        bm
bm-R3_1.fp.fq.gz        bm-R3_2.rp.fq.gz        bm
dpi8-R1_1.fp.fq.gz  dpi8-R1_2.rp.fq.gz  dpi8
dpi8-R2_1.fp.fq.gz  dpi8-R2_2.rp.fq.gz  dpi8
dpi8-R3_1.fp.fq.gz  dpi8-R3_2.rp.fq.gz  dpi8
dpi12-R1_1.fp.fq.gz     dpi12-R1_2.rp.fq.gz     dpi12
dpi12-R2_1.fp.fq.gz     dpi12-R2_2.rp.fq.gz     dpi12
dpi12-R3_1.fp.fq.gz     dpi12-R3_2.rp.fq.gz     dpi12
dpi22-R1_1.fp.fq.gz     dpi22-R1_2.rp.fq.gz     dpi22
dpi22-R2_1.fp.fq.gz     dpi22-R2_2.rp.fq.gz     dpi22
dpi22-R3_1.fp.fq.gz     dpi22-R3_2.rp.fq.gz     dpi22
c1_1.fp.fq.gz   c1_2.rp.fq.gz   control
c2_1.fp.fq.gz   c2_2.rp.fq.gz   control
c3_1.fp.fq.gz   c3_2.rp.fq.gz   control
c4_1.fp.fq.gz   c4_2.rp.fq.gz   control
c5_1.fp.fq.gz   c5_2.rp.fq.gz   control
c6_1.fp.fq.gz   c6_2.rp.fq.gz   control
c7_1.fp.fq.gz   c7_2.rp.fq.gz   control
c8_1.fp.fq.gz   c8_2.rp.fq.gz   control
c9_1.fp.fq.gz   c9_2.rp.fq.gz   control
c10_1.fp.fq.gz  c10_2.rp.fq.gz  control
c11_1.fp.fq.gz  c11_2.rp.fq.gz  control
c12_1.fp.fq.gz  c12_2.rp.fq.gz  control

Is there any way to "explain" to FeatureCounts that in that BAM file there are so many samples?

Thanks in advance

Answer 1

[antonioggsousa]

I never run it myself, but I believe that input_file1 is not a parameter. It appears in the documentation to exemplify that you need to provide there the input file. So, remove that and let only the bam file as input_file1, like this:

featureCounts -a /path/to/genome_reference/GCF_000209185.1_CulPip1.0_genomic.gff -o Table.count Aligned_mosquito.out.bam

Notice that all the parameter options start with minus - plus one letter, which is not the case of input_file1.

I hope this solves your problem,

António

[luzglongoria]

OMG!!!! I feel so stupid!!! thank you so much! It solved the problem

[ATpoint]

Please accept the answer if helpful (the green checkmark symbol left of his answer).