salmon kallisto sleuth results in a genome browser ?

Question

[carlmannfr]

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 ?

Answer 1

[Istvan Albert]

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

[Rob]

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.