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salmon kallisto sleuth results in a genome browser ?

For differentially-expressed transcripts identified by salmon/kallisto-sleuth, is there was any way to retrieve the alignments so that they could be viewed in a genome brower, or is it necessary to independently map in parallel all the seq reads to the genome in order to get the alignments ?

rna-seq
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updated by Istvan Albert Istvan Albert • written by carlmannfr • carlmannfr

1 answer

There is a --pseudobam option to kallisto quant that may produce the output that you want:

Usage: kallisto quant [arguments] FASTQ-files
   ....
   --pseudobam               Output pseudoalignments in SAM format to stdout
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written by Istvan Albert Istvan Albert

Just for future reference, this can also be done with salmon using the --writeMappings flag. However, it's probably worth noting that the pseudo-SAM files produced by these programs are mapping records of fragments directly to the transcriptome (and before probabilistic assignment). Thus, there will be quite a lot of multi-mapping, and the coordinates are with respect to individual transcripts, not the genome.

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written by Rob Rob

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