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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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Should I sort the merged BAM file after combining all the sorted BAM files? #436

Open YIGUIz opened 4 months ago

YIGUIz commented 4 months ago

Hi, I'm going to assemble transcripts by each tissue. Firstly, I'll merge all sorted bam files form the same tissue. and then use the merged bam file to get the final gtf file. My question : Should I sort the merged BAM file after combining all the sorted BAM files?

Here is my command:

samtools merge ${TISSUE}_SR_sorted.bam $(echo ${SR_bams[@]}) samtools merge ${TISSUE}_LR_sorted.bam $(echo ${SR_bams[@]})

stringtie -o ${TISSUE}_mix_tissue.out.gtf --mix -p ${threads} -G ${genome_gff} ${TISSUE}_SR_sorted.bam ${TISSUE}_LR_sorted.bam

Thank you!