Open FaehlingT opened 2 years ago
When I ran A3 like described, it failed because of missing spatial coordinates. I then addad --spatial with the path to the spatialcoordinates.txt file from A2 (step2 in the example dataset - because the file wasn't in step3 folder) and it worked.
python3 $STHOME/sttools.py --run-steps A3 --STtools $STHOME \ --whitelist $STWHITELIST/whitelist.txt \ --second-fq1 $STDATA/step3_align/liver_tile2106_sub_R1.fastq.gz \ --second-fq2 $STDATA/step3_align/liver_tile2106_sub_R2.fastq.gz \ --outdir $STOUT --genome $GENOMEINDEX \ --star-path $STARPATH --seqtk-path $SEQTKPATH \ --spatial /path/to/spatialcoordinates.txt \
Is this the right solution or is something wrong with the code? Thanks!
When I ran A3 like described, it failed because of missing spatial coordinates. I then addad --spatial with the path to the spatialcoordinates.txt file from A2 (step2 in the example dataset - because the file wasn't in step3 folder) and it worked.
python3 $STHOME/sttools.py --run-steps A3 --STtools $STHOME \ --whitelist $STWHITELIST/whitelist.txt \ --second-fq1 $STDATA/step3_align/liver_tile2106_sub_R1.fastq.gz \ --second-fq2 $STDATA/step3_align/liver_tile2106_sub_R2.fastq.gz \ --outdir $STOUT --genome $GENOMEINDEX \ --star-path $STARPATH --seqtk-path $SEQTKPATH \ --spatial /path/to/spatialcoordinates.txt \
Is this the right solution or is something wrong with the code? Thanks!