Closed jeremyadamsfisher closed 2 years ago
This should be fixed in the latest dev
version.
This is actually NOT fixed in the latest dev version, as I get
EXITING because of FATAL ERROR in input read file: the total length of barcode sequence is 28 not equal to expected 26
Read ID=@A01174:218:HKWM7DSX2:4:1101:1036:1063 ; Sequence=CTCATTACACGTACATGCGGGTTTGCCG
SOLUTION: check the formatting of input read files.
If UMI+CB length is not equal to the barcode read length, specify barcode read length with --soloBarcodeReadLength
To avoid checking of barcode read length, specify --soloBarcodeReadLength 0
Jun 14 13:07:28 ...... FATAL ERROR, exiting
with a v3 library.
(v3 has 28nt barcode+umi, compared to 26 in v2)
We should get this fix into 2.0.0 too in my opinion :-(
The default barcode lengths (CB=16b, UMI=10b) work for 10X Chromium V2. For V3, specify:
--soloUMIlen 12
I think this parameter is missing. Should be somehow generated by the java code in the lib
folder.
Should be fixed in #113 now
Check Documentation
I have checked the following places for your error:
Description of the bug
STARsolo uses 10X-V2 chemistry, regardless of what is specified.
Steps to reproduce
Steps to reproduce the behaviour:
nextflow run nf-core/scrnaseq -r 1.1.0 -params-file nf-params.json
nf-params.json
Where:
genome.fa
is fromhttp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/GRCm39.genome.fa.gz
;genes.gtf
is fromhttp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/gencode.vM27.annotation.gtf.gz
; and the fastq files are fromhttps://www.ncbi.nlm.nih.gov/sra/?term=SRR14597268
Expected behaviour
According to the STAR readme,
This option is not specified by the pipeline. The STAR script should differ by the chemistry, as per https://www.biostars.org/p/462568/
Log files
nextflow.log
System
Nextflow Installation
Container engine
Additional context
Would be happy to write a PR