Hi I am processing the sn-RNA fastq files, and I can't find any barcode files, do you guys know where I can find it?

Created by Junming Hu hjunming
it's working right now! Thanks for your help!
Sure! I will test it right now!
Hi Junming, the new (non-truncated) file has been uploaded. Could you let us know if there are any issues processing it now? Thanks.
Appreciate for your help!
Hi Junming, you're right - the contents of this file appear to be truncated. Thanks for bringing it to our attention. We will replace this file with the full version and let you know when it's done, so you can test it.
Just that one
Hi Junming, thanks for letting us know. Is it only this file that leads to this Cellranger processing error? Or do you get this error when you run Cellranger for every file you've downloaded?
Hi Mette, I meet some problem when I processed the MFC-B1-S1-Cdx1-pAD0-R2.fastq.gz files, I try to download again for this data, and it always give me an error list below, Log message: Traceback (most recent call last): File "/restricted/projectnb/casa/jmh/rosmap_scRNAseq/code/cellranger-3.0.2/martian-cs/v3.2.0/adapters/python/martian_shell.py", line 590, in _main stage.main() File "/restricted/projectnb/casa/jmh/rosmap_scRNAseq/code/cellranger-3.0.2/martian-cs/v3.2.0/adapters/python/martian_shell.py", line 555, in main self._run(lambda: self._module.main(args, outs)) File "/restricted/projectnb/casa/jmh/rosmap_scRNAseq/code/cellranger-3.0.2/martian-cs/v3.2.0/adapters/python/martian_shell.py", line 524, in _run cmd() File "/restricted/projectnb/casa/jmh/rosmap_scRNAseq/code/cellranger-3.0.2/martian-cs/v3.2.0/adapters/python/martian_shell.py", line 555, in self._run(lambda: self._module.main(args, outs)) File "/restricted/projectnb/casa/jmh/rosmap_scRNAseq/code/cellranger-3.0.2/cellranger-cs/3.0.2/mro/stages/common/chunk_reads/__init__.py", line 53, in main tk_subproc.check_call(chunk_reads_args) File "/restricted/projectnb/casa/jmh/rosmap_scRNAseq/code/cellranger-3.0.2/cellranger-cs/3.0.2/tenkit/lib/python/tenkit/log_subprocess.py", line 37, in check_call return subprocess.check_call(*args, **kwargs) File "/restricted/projectnb/casa/jmh/rosmap_scRNAseq/code/cellranger-3.0.2/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/lib/python2.7/subprocess.py", line 186, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command '['chunk_reads', '--reads-per-fastq', '5000000', 'rosmap_scRNAseq/fastq/syn17055069/MFC-B1-S2-Cdx1-pAD0-M-counts/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u3ec351b79e/files/', 'fastq_chunk', '--martian-args', 'chunk_args.json', '--compress', 'lz4']' returned non-zero exit status 1. I follow the script you offer online. But it's not work for this one. #!/bin/bash -l runDir=rosmap_scRNAseq/fastq/syn17055069 software=rosmap_scRNAseq/code/cellranger-3.0.2/cellranger-cs/3.0.2/bin cd $runDir $software/cellranger count --id=MFC-B1-S2-Cdx1-pAD0-M-counts \ --fastqs=rosmap_scRNAseq/fastq/syn17055069 \ --transcriptome=rosmap_scRNAseq/code/gtf/refdata-cellranger-GRCh38-3.0.0 \ --sample=MFC-B1-S2-Cdx1-pAD0-M Can you check if I do something wrong with the code or something wrong with the file? Many thanks Junming
@hjunming - the index files are now public. See here: syn16780177 (index folder). Note data processing instructions added to the assay wiki
Vilas has uploaded the index files and instructions. We need to review before making them public. Will provide you an update once that's done
Hi I just wanna check if you update the files. Or if you can send me via email. My email address is hjunming@bu.edu Thx
Great? I am really appreciate about what you will do for me!
Hi Junming - thanks for pointing this out. The index files are missing, so I will upload them, as well as more detailed instructions on how to process the fastq files with cellranger.
@vilasmenon - can you answer the question about the availability of the barcodes for the ROSMAP single cell RNAseq. Thanks! Mette
The synID is syn16780177, Thanks!
Can you please reference the synID for the data

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