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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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Hello!
I'm building a ctat_genome_library in preparation to run STAR-Fusion, but I came across an error when I ran "prep_genome_lib.pl". It ran into an issue when trying to run "index_pfam_domain_…
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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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RefSeq transcript sequences can be different from the reference sequence (even if they agree with 1 build they can be different across builds). These sequences are aligned against the genome to produc…
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Hi,
I encountered some errors when using sRNAbench from the srnatoolbox container. It says "bowtie --quiet was not found to be installed. Please install first. Will quit now!." When I checked the p…
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p100のkallisto.idxの作成コマンド以下を試しましたがerrorがでました。
kallisto index --index=~/Documents/expression/ref/kallisto.idx ~/Documents/expression/ref/Homo_sapiens.GRCh38.cdna.all.fa.gz
[build] loading fasta file…
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Hi,
I have a bam file (nanopore transcripts) aligned to cdna and I need to convert it to genomic coordinates. Is there a way to use ensembldb to do that? Kindly let me know.
Thanks