Question: salmon kallisto sleuth results in a genome browser ?
gravatar for carlmannfr
3.0 years ago by
carlmannfr0 wrote:

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 • 844 views
ADD COMMENTlink modified 3.0 years ago by Istvan Albert ♦♦ 84k • written 3.0 years ago by carlmannfr0
gravatar for Istvan Albert
3.0 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

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
ADD COMMENTlink written 3.0 years ago by Istvan Albert ♦♦ 84k

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.

ADD REPLYlink written 3.0 years ago by Rob4.0k
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