Entering edit mode
4.1 years ago
evelyn
▴
230
Hello,
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 \
I=out.sorted.bam \
O=out_marked_duplicates.bam \
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!
Everything you need to know is listed in the documentation: https://salmon.readthedocs.io/en/latest/salmon.html#quantifying-in-alignment-based-mode
I do not see any specific question, is there any? Also, why aligning data if you end up using
salmon
?salmon
can use fastq rigth away.Thank you! I want to see any difference using this approach as compared to using fastq files. I could not find an option for light weight alignment in the documentation.
as a side note: I would not blindly remove duplicates if your goal is expression analysis. It might bias your analysis.
I am not going to remove the duplicates. I am looking for a way to use salmon alignment for sorted bam files created with hisat2 including the reference genome.