Hi Biostars,
I try to get the loom file to do velocity analysis:
velocyto run10x -m Hg38_rmsk.gtf WT/outs /cellranger/reference/refdata-cellranger-GRCh38-3.0.0/genes/genes.gtf
Inside WT/outs I have some folders such as filtered_feature_bc_matrix. Inside filtered_feature_bc_matrix, I have barcodes.tsv.gz
ERROR - This is an older version of cellranger, cannot check if the output are ready, make sure of this yourself.
ERROR - Can not locate the barcodes.tsv file!
line 91, in run10x.
bcfile = bcmatches[0].
IndexError: list index out of range.
Would you please have a suggestion? Thank you so much!
Update: I added the bam file and rename it to: possorted_genome_bam.bam then:
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
1 answer
Unfortunately, I got a new error:
MemoryError: bam file #0 could not be sorted by cells.
This is probably related to an old version of samtools, please install samtools >= 1.6. In alternative this could be a memory error, try to set the --samtools_memory option to a value compatible with your system.
Otherwise sort manually by samtools sort -l [compression] -m [mb_to_use]M -t [tagname] -O BAM -@ [threads_to_use] -o cellsorted_[bamfile] [bamfile]
I have samtools 1.9 and ran this:
velocyto run -b MT/outs/filtered_feature_bc_matrix/barcodes.tsv -o output_dir -m Hg38_rmsk.gtf MT/outs/possorted_genome_bam.bam /cellranger/reference/refdata-cellranger-GRCh38
-3.0.0/genes/genes.gtf --samtools-memory 4000 --samtools-threads 8
Log in to answer this question.
-
Discrepancy in gene expression between cellranger and velocyto pipeline
written by sarang.chafle •
-
In need of help with my RNA velocity trajectory inference pipeline!
written by phhelou5 •
-
Help with error velocyto
written by Chris •
-
Need help with Velocyto Analysis. Errors: MemoryError: bam file #0 could not be sorted by cells.
written by Anna •
-
Tools to generate spliced/unspliced counts
written by PianoEntropy •
-
Disappearing CB, the bam tag after samtools sort -t CB
written by akh22
-
Cellranger count fails at mapping
written by gnomee •
Is there a
WT/_versionsfile? Also, what is the version of velocyto you're using?No, I don't have
_versionsinsideWT. I. think it is 0.17.17. I also have another folderMT.Cellranger produces some files with runtime parameters and settings and dumps them in the same directory as the
outsdirectory. Also, please don't guess versions - double check and add what you can verify. I cannot help you with velocyto but any software issue can only benefit from exact version info.Yes, I checked. It is
0.17.17.