Question: Kallisto "pseudo" output to counts/expression matrix
gravatar for paulranum11
10 days ago by
paulranum1130 wrote:

Is there a tool available that will convert the output of kallisto "pseudo" (matrix.tsv,, and matrix.cells) into a standard genes by cells counts matrix?

rna-seq alignment • 165 views
ADD COMMENTlink modified 10 days ago by h.mon24k • written 10 days ago by paulranum1130

May be something - could contact the Pachter lab directly. They are not regulars here on Biostars.

Other options:

  • import into DESeq2 using tximport (you'll just need to make a file listing, and then tximport will do most of the heavy lifting)
  • paste relevant columns together yourself into a matrix
ADD REPLYlink written 10 days ago by Kevin Blighe39k

The output of kallisto "pseudo" is formatted differently than the output of other kallisto runs i have performed in the past (kallisto "quant" etc). The output appears to be associative arrays (matrix.tsv,, and matrix.cells). Here are some examples:


12531   0   1
18862   0   1
384133  0   1
138357  1   1
199880  1   1
422948  1   1
51111   2   1


422968  22108,80043,80044,84616,91003,93151,93152,93153,93154
422969  939,941,950,974,1125,4632,102217,102409,113753,113766,115246,115359
422970  102268,102280,108561,110740,114873
422971  91677,91680
422972  66108,66109,76096
422973  8687,8688,39455
422974  15300,18434,40489,94720
422975  58132,103245,104106,105656,106906,109217,109621,109756,109846,109853,109855,110441,111708,112144
422976  6117,6118,80071,90398
422977  19697,60885,68905



I took a look at using tximport but it appeared to me to be better suited for the output of kallisto "quant" it was not clear where i would begin with the output of kallisto "pseudo". Are there any examples availible for running tximport with this style of input?

ADD REPLYlink modified 10 days ago • written 10 days ago by paulranum1130

I would contact the Pachter group.

ADD REPLYlink written 10 days ago by Kevin Blighe39k
gravatar for h.mon
10 days ago by
h.mon24k wrote:

The R/BioConductor tximport can do this.

ADD COMMENTlink written 10 days ago by h.mon24k

tximport does not support this kallisto "pseudo" format output.

ADD REPLYlink written 10 days ago by paulranum1130

There is a suggestion to use python at the kallisto-sleuth-users list:

kallisto pseudo output

ADD REPLYlink modified 9 days ago • written 9 days ago by h.mon24k
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