Question: rna paired sequence sort is important
0
gravatar for sarfrajiiet
14 months ago by
sarfrajiiet0 wrote:

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

rna-seq alignment sequence • 287 views
ADD COMMENTlink modified 13 months ago by WouterDeCoster44k • written 14 months ago by sarfrajiiet0

Please add some punctuation and write in separate sentences. This is barely readable.

mapped it with hg38 bowtie2 index

bowtie2 does not due spliced alignment, but you did not tell us which organism you are working on. For eukaryotic organisms, STAR or HISAT2 would be a better choice.

is it important to sort it for htseq count

Yes. A better tool would be featureCounts.

ADD REPLYlink written 14 months ago by WouterDeCoster44k
0
gravatar for WouterDeCoster
13 months ago by
Belgium
WouterDeCoster44k 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.

ADD COMMENTlink written 13 months ago by WouterDeCoster44k
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