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Old 04-09-2019, 12:19 PM   #1
JeremyDay
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Location: San Diego

Join Date: Feb 2012
Posts: 25
Default No bam from kallisto or Salmon after piping into samtools

Hi all,

I am trying to generate the pseudo bam files from both Kallisto v45 and Salmon v13 and can't get either to pipe into Samtools and generate a non-emtpy file. I think I am more currently focused on Salmon since I am getting good mapping results with it, but I've tried with Kallisto also just to see if I can generate the file.

In my script:

salmon quant -i $SalmonIndex -l A -1 $fq1 -2 $fq2 -p 20 -o `pwd` --validateMappings --writeMappings | samtools view -bS - > SalmonBamTest.bam

kallisto quant -i $KallistoIndex -o ./$out --threads=40 --bias --single-overhang $SPECIFICITY --pseudobam $fq1 $fq2 | samtools view -bS - > kallistoPseudobam.bam

Kallisto will run but I get an empty bam file.
Salmon stops after 'Index contained 137,271 targets' and goes to the command prompt, also an empty file I believe

If I remove the pipe and add writeMappings=SalmonBamTest.sam, I generate a sam file that can then be converted with the samtools view command. I realize I can do this in my script and delete the sam, but it's killing me that I can't get the direct pipe into samtools working.
Does anyone have any clue what I am doing wrong?

Thank you!
Jeremy
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