Total Alignment: 0 /results of featureCounts RNA-Seq
0
0
Entering edit mode
4 months ago
santos48 ▴ 30

I have human RNA-Seq dataset it has two different barcodes in the different folder. I aligned with that command minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam I try to quantify and counts using with Subread featureCounts function. In the subread results, there is a problem with one of the bam files. I downloaded reference and gtf files from GENCODE. I checked the bam file with samtools view -H first.bam-second.bam I saw that I followed the same steps for each bam file. In the IGV results, I saw matches and alignment for all bam files.

Do you have any suggestions the solve this problem? What am I doing wrong?

featureCounts -T 8 -a gencode.v38.chr_patch_hapl_scaff.annotation.gtf -g 'transcript_id' -o readcouts.txt bam/*.bam

|| Total alignments : 11214480 ||
|| Successfully assigned alignments : 4051945 (36.1%) ||
|| Running time : 2.67 minutes

|| Total alignments : 0 ||
|| Successfully assigned alignments : 0 ||
|| Running time : 2.89 minutes

I also tried with Salmon in the salmon alignment-based quantification results bam file has huge differences between each other.

`salmon quant --ont -t reference.fa -l A -a first.bam -o salmon_quant1`

Total # of mapped reads : 5465357

of uniquely mapped reads : 328808350000000

ambiguously mapped reads : 2177274
`salmon quant --ont -t reference.fa -l A -a second.bam -o salmon_quant2`
Completed first pass through the alignment file.

Total # of mapped reads : 3843632

of uniquely mapped reads : 2552463

ambiguously mapped reads : 1291169
Nanopore featureCounts HG38 Rna-Seq • 180 views
ADD COMMENT
1
Entering edit mode
ADD REPLY

Login before adding your answer.

Traffic: 2495 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

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

Powered by the version 2.3.6