STARsolo output formatting issues

[vpresnyak]

Hi @alexdobin,

I'm testing STARsolo for our single-cell use and have run into some issues using the output for downstream analysis. The formatting of the files does not match that of the Cellranger outputs and trips up tools that expect those files as input (e.g. scanpy).

The formatting of genes.tsv seems unusual - it looks like the information alternates between columns. This isn't the case in Cellranger output files:

$ cat ./Solo.out/genes.tsv | head 
ENSG00000223972.5       DDX11L1
WASH7P  ENSG00000278267.1
ENSG00000243485.5       MIR1302-2HG
MIR1302-2       ENSG00000237613.2
ENSG00000268020.3       AL627309.6
OR4G11P ENSG00000186092.5
ENSG00000238009.6       AL627309.1
AL627309.3      ENSG00000233750.3
ENSG00000268903.1       AL627309.7
AL627309.8      ENSG00000239906.1

As a separate issue, the matrix.mtx file is missing its header. This seems to be required by the file type definition (https://math.nist.gov/MatrixMarket/formats.html) and is checked by tools that read the file (cellranger outputs provided for comparison).

$ cat ./Solo.out/matrix.mtx | head
%%
%
58347 737280 6489398
17075   1       1
22155   1       1
40733   1       1
44903   1       1
48401   1       1
50993   1       2
55467   8       1

$ gunzip -c cell_ranger/outs/raw_feature_bc_matrix/matrix.mtx.gz | head
%%MatrixMarket matrix coordinate integer general
%metadata_json: {"format_version": 2, "software_version": "3.0.1"}
33538 737280 6251612
9817 1 1
10931 1 1
12597 1 1
24283 1 1
26812 1 1
28909 1 1
31584 1 2

I'm not sure if I'm doing something funny at the command line, here's how I'm running it:

STAR --soloType Droplet --runThreadN 64 --soloCBwhitelist /scratch/cellranger-2.1.1/cellranger-cs/2.1.1/lib/python/cellranger/barcodes/737K-august-2016.txt --outFileNamePrefix . --genomeDir /scratch/temp_genome --readFilesCommand gunzip -c --readFilesIn ...

[alexdobin]

Hi @vpresnyak

have you re-generated the genome index with the 2.7.0a version?
It's supposed to throw an error with an old genome, but maybe that did not work.

There is pull-in request for the matrix header change, I will make a patch tonight.

Cheers
Alex

[vpresnyak]

The genome reference was generated fresh from the GRCh38 gencode files. I did try running it with an older genome, which threw an error as it's supposed to.

[alexdobin]

Thanks!

I think I found the problem, please try the patch I just uploaded to GitHub master.
I will make a tagged release tomorrow, hopefully.

[bgruening]

We think this can be closed ... isn't it?

[alexdobin]

It should be working, but I did not hear back from the OP.
Let's close it.