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Hi, I run the PASA in docker, when using the "/usr/local/src/PASApipeline/scripts/build_comprehensive_transcriptome.dbi" tools with the defaults parameters, however, this error appeared.
Limited err…
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**Describe the bug**
According to [the documentation](https://agat.readthedocs.io/en/latest/tools/agat_sp_extract_sequences.html#agat-sp-extract-sequences-pl), the headers created by the script are f…
jdcla updated
5 months ago
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CellBase (for Transcripts ONLY) is sorting after the pagination. It must sort before the SKIP and LIMIT are being applied. If there is a replicaset present, then the query results will be incorrect.
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Hello!
I'm new to using Trinity! My goal is to obtain the translated protein sequence of a specific gene. My organism is non-model but does have a genome, so I used the reference-based assembly. Af…
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I am trying to use the beta functions
but facing this error (log below), any ideas how to pr…
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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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After quantification I tried simulating
IDs in expression profile:
NM_001001130.3
IDs in reference:
\>NM_001001130.3 Mus musculus zinc finger protein 85 (Zfp85), mRNA
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Hi Brian,
I've run EVM with a genome around 1.2Gb, with over 100K gene predictions from Braker, and two transcript assemblies, it has been running for over 1 week, now occupied 400Gb RAM.
Maybe I…
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```text
$ time seqconv convert --ref felCat4 --out rs cat_felCat4_UCSC_2008.gtf >test_cat_4.rs.gtf
Converting from None to rsStarting Conversion
Cannot convert id: chrM
No corresponding id for ch…
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Hello Pierre,
I was able to run Viral-Track successfully. However, I noticed that if you don't run the transcriptome assembly step `Viral_Track_cell_demultiplexing.R` crashes because the basic GTF …