BACKGROUND:
I have RNA-Seq data from Illumina platform.
I aligned the reads post-QC onto hg19 bowtie index using tophat.
Now I wished to get the raw count of reads mapped to each gene using Ht-seq-count.
WHAT I DID:
However the HT-Seq reports error that it is unable to find the mate pair and asks whether the sam file is properly sorted.
Hence, after reading posts on the problem. I sorted my bam files using samtoools.
samtools sort -n accepted_hits.bam accepted_hits_bam_sorted
CONCERN:
Now the sorted BAM file has increased in size and I wish to know why his has happened.
Though it might not be but seems highly unintuitive.
I have RNA-Seq data from Illumina platform.
I aligned the reads post-QC onto hg19 bowtie index using tophat.
Now I wished to get the raw count of reads mapped to each gene using Ht-seq-count.
WHAT I DID:
However the HT-Seq reports error that it is unable to find the mate pair and asks whether the sam file is properly sorted.
Hence, after reading posts on the problem. I sorted my bam files using samtoools.
samtools sort -n accepted_hits.bam accepted_hits_bam_sorted
CONCERN:
Now the sorted BAM file has increased in size and I wish to know why his has happened.
Though it might not be but seems highly unintuitive.
Comment