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Hi Alex,
What causes blank (dash) UB tags when the CB tag has a normal barcode sequence? The R1 (barcode+UMI) read looks like any other read, but I noticed that the R2 (cDNA) read is low quality. I…
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Hello,
Our lab currently trying the cDNA-PCR barcoding kit (PCB111.24) for our _de novo_ assembly transcriptome project. Our issue is that after using pychopper, we still somehow have the barcode se…
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When I installed arcasHLA through conda and ran the code, the following error occurred.
`(JS) seokjune@workstation:~/JSP$ arcasHLA genotype -t 8 -o arcas_RE-P220-T --log log.arcas_RE-P220-T.txt /ho…
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I was wondering if there was a way or specification for SAM headers to describe what custom tags they are using, for example the lower case and X/Y/Z prefixed tags. My angle on this is just showing us…
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Dear Liz,
When running cDNA_cupcake, I'm encountering the following error:
> Traceback (most recent call last):
File "collapse_isoforms_by_sam.py", line 62
Print(“picking representative sequen…
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Hi there, I was wondering what the difference between RTP/ VN and a forward primer is based on the 10x - 3' protocol doc.
The TSO in my protocol seems to match the one in the restrander config file.…
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Hi,
I'm running into an issue with assemble_clusters.dbi getting this error:
`* [Mon Jan 24 12:55:33 2022] Running CMD: /Users/jadem/Documents/scripts/PASApipeline/scripts/assemble_clusters.dbi -…
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I have mapped Oxford Nanopore Reads to transcriptome using Graphmap. When I tried to run salmon quant on the BAM file, it shows that error below:
```
salmon quant -t GRCh37.67.cdna.all.fa -l A -a …
EPKok updated
5 years ago
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Dear Mark,
Validation seems to fail for Mouse dRNA ONT + cDNA Illumina (long_short) submission.
When a single Mouse ES sample is provided in the entry.json, the following message is reported:
`…
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Hi,
I'm trying to download a subset of the 1D cDNA dataset using the links given here https://github.com/nanopore-wgs-consortium/NA12878/blob/master/nanopore-human-transcriptome/fastq_fast5_bulk.md…