Gtf/gff file in featurecounts
Hello, I am working on stickleback RNAseq data. I want to count reads for each gene. But i am not getting Successfully assigned reads in featurecount. The .gtf file i am using from
ftp://ftp.ensembl.org/pub/release-100/gtf/gasterosteus_aculeatus/
Can anyone let me know if the .gtf file is workable?
• 3,961 views
•
link
written
by
baurumon •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Which reference genome file is correct?
written by theodore.killian •
-
repeatmasker .out files of Mus_musculus.GRCm38.dna_rm
written by toyo •
-
Where can I download the gff3 file for a specific human genome build? (hg38 release 77)
written by O.rka
-
ENSEMBL annotation file for quantification: which file to use?
written by psm
-
Drosophila genome indexing using STAR for mapping reads
written by ishento •
-
Fasta file and GTF file for STAR alignment
written by snp87 •
-
Source of bed file
written by Arindam Ghosh
-
No XIST in Emsembl cdna.fa
written by WouterDeCoster
-
GTF file problem
written by johnsonn573 •
-
peak annotation chip-seq
written by ana222 •
Please add code and summary statistics, anecdotal descriptions are hard to debug.
Hi I have used this code featureCounts -T 5 -t exon -g gene_id -O -a reference_trans/corrected.gtf -b -o Counts_SRR1390636.txt SRR1390636_sorted.bam
Output description link below
enter link description here
Thanks
Ok, did you check if the chromosome names are the same between your BAM and your GTF?
Chromosomes name of these two files are different.
enter link description here
enter link description here
There is your reason why nothing can be mapped.