Problem when running FeatureCounts
Entering edit mode
6 months ago
luzglongoria ▴ 40

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

FeatureCounts BAMfile RNA-Seq RNA Error • 459 views
Entering edit mode
6 months ago
antonioggsousa ★ 2.1k

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,


Entering edit mode

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

Entering edit mode

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


Login before adding your answer.

Traffic: 2798 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6