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```bash
ImportError: cannot import name 'run_find_by_type' from 'seqspec.seqspec_find' (/uoa/scratch/users/s14dw4/.conda/envs/cellatlas_fork/lib/python3.7/site-packages/seqspec/seqspec_find.py)
```
…
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Hi,
I'm trying to combine my TACO output and TD output within this command but it returns error:
`$TD_PATH/util/cdna_alignment_orf_to_genome_orf.pl longest_orfs.cds.transdecoder.gff3 ../TACO/out…
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#### Issue description
There is Order-Dependent flakiness in this testing code. The test will fail on the exact 36th run on a continual run.
#### Steps to reproduce the issue
1. run pytest…
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Chemistry(darkreaction) determined in oligoR1: darkreaction
Chemistry(darkreaction) determined in oligoR2: darkreaction
Chemistry(darkreaction) determined in cDNAR1 : darkreaction
2024-11-07 00:0…
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In my use I add a FASTA asset (a secondary one) like:
```
refgenie build homo_sapiens--GRCh38/fasta:cdna_ensembl95 --files fasta=Homo_sapiens.GRCh38.cdna.all.95.fa.gz
```
That works:
```
>…
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I'm trying to use STARsolo to analyze novel scRNAseq data using techniques such as scFAST-seq or snRandom-seq. The principle is basically the same, using random primers to capture single cells. Its pa…
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My libraries were build using the 10X Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1.
My Read 1 sequence looks like this:
@A00738:420:HY77NDSX3:3:1101:1217:1000 1:N:0:CGGAACCCAA+TCCTCGAATC
…
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As part of #2046 we are moving from ``Seq`` objects having an alphabet object from ``Bio.Alphabets``, to recording the molecule type in the ``SeqRecord`` annotations instead. Currently this recycles t…
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Hi!
I am getting an error when converting the `graphmap2` (v 0.6.0) generated sam file (of nanopore cDNA reads mapped to a reference assembly) to bam.
These are the logs of the run:
> [22:32:…
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Hello,
when using Pizzly 0.37.3 (SeqAn 2.2.0) and Kallisto 0.43.1 with Ensembl 81 and one gets this error message from Pizzly:
```
Error, could not find any transcript sequences check that the i…