i have rna paired fasta file I trimmed it using trim galore and then mapped it with hg38 bowtie2 index now i have sam file is it important to sort it for htseq count i have to ask that the process that i follow till now is it correct differential expression and second that what next to do to get differential expression i m new please help me
Question: rna paired sequence sort is important
14 months ago by
sarfrajiiet • 0
sarfrajiiet • 0 wrote:
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13 months ago by
WouterDeCoster ♦ 44k
WouterDeCoster ♦ 44k wrote:
is it important to sort it for htseq count
Yes you should (always) sort your bam files.
Note that you can often do this directly after alignment without creating intermediate files:
aligner genome.fasta reads1.fasta.gz reads2.fastq.gz | samtools sort -o sorted_alignment.bam
A better tool for counting expression levels would be featureCounts.
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