Entering edit mode
7.5 years ago
zizigolu
★
4.3k
hi,
I want to count the miRNA reads using the sorted .bam file containing only mapped reads (all generated by samtools from Bowtie output --SAM file) by featurecounts for Aspergillus fumigatus but the number of reads for all of the gene_ids are zero, what happened? :(
this is my command
featureCounts -t exon -g gene_id -a annotation.gtf -o counts.txt mapping_results_SE.bam
I downloaded genome fasta and GTF from esembl
What is printed on the screen ? It prints the log information on terminal.
Whats the output of following commands ?
'
exon
' and 'gene_id
' are default parameters anyway.first I removed unmapped reads by
samtools view -S -h -F 4 -q 42
then converted to bam
samtools view -b -S
then sorting bam
samtools sort
It would be useful if you provide the information asked for.
sorry Goutham I am with remote access then took long time to provide commands
Hmm, those should be getting counted. Hopefully the
-R
option will clarify things.thank you,
you mean I should -R in the same screen I am running featurecounts?
You should use that option in featureCounts.
You might try the
-R
option, the resulting file will note for each alignment/pair why they weren't included. Note that this will be a really big text file, so maybe eyeball some alignments that you think should be getting counted and make a BAM file containing only them.sorry in ensembl there are 4 Aspergillus fumigatus, I only received linke for downloading fastq files, might be the errors is because of outmatching between fastq files and genome fasta???
No, fastq files don't have associated genomes.