Question: Kallisto "pseudo" output to counts/expression matrix
0
gravatar for paulranum11
8 months ago by
paulranum1140
paulranum1140 wrote:

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

rna-seq alignment • 581 views
ADD COMMENTlink modified 8 months ago by h.mon28k • written 8 months ago by paulranum1140
1

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 8 months ago by Kevin Blighe51k

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, matrix.ec, and matrix.cells). Here are some examples:

matrix.tsv

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

matrix.ex

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

matrix.cells

cell_001
cell_002
cell_003
cell_004
cell_005

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 8 months ago • written 8 months ago by paulranum1140

I would contact the Pachter group.

ADD REPLYlink written 8 months ago by Kevin Blighe51k
1
gravatar for h.mon
8 months ago by
h.mon28k
Brazil
h.mon28k wrote:

The R/BioConductor tximport can do this.

ADD COMMENTlink written 8 months ago by h.mon28k

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

ADD REPLYlink written 8 months ago by paulranum1140

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

kallisto pseudo output

ADD REPLYlink modified 8 months ago • written 8 months ago by h.mon28k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1773 users visited in the last hour