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8 hours ago by


I have sorted bam files for paired end RNA seq fastq files using Hisat2, Picard and I want to use salmon alignment mode:

hisat2 -q -x genome -1 input_1.fastq -2 input_2.fastq -S out.sam
samtools view -bS out.sam > out.bam
samtools sort out.bam -o out.sorted.bam
samtools index out.sorted.bam

java -jar picard.jar MarkDuplicates 
java -jar picard.jar BuildBamIndex  INPUT=out_marked_duplicates.bam

Then to use salmon,

salmon quant -t transcripts.fa -l -A -a out_marked_duplicates.bam -o salmon_quant

I am not sure if there is any different option for using this sorted bam file for salmon. I will appreciate any comments/help! Thank you!

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