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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Question: Does the bam file needs indexing ? #266

Closed Tdanis closed 4 years ago

Tdanis commented 4 years ago

Hello, I am taking the out sam file from my mapper and I am trying to convert it in bam format.

The command that I am using is this:

/mnt/big/Tools/samtools-1.9/samtools view -S(b)u -@20 Aligned.out.sam > alg.bam

/mnt/big/Tools/samtools-1.9/samtools sort alg.bam -@20 -o ./alg.sorted.bam

/mnt/big/Tools/samtools-1.9/samtools index alg.sorted.bam

is it correct? or indexing step is unnecessary?

Thank you

gpertea commented 4 years ago

StringTie does not need or use a BAM index.