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Hi all,
I am writing to ask your thoughts about how to deal with transdecoder output with strings of N's in the CDS fasta, that get turned into strings of X's for the longest_orfs.pep that we use a…
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Hello all, thanks for squanti.
We've written an end-to-end isoseq pipeline that uses squanti, and as part of that I'm making a bioconda package for squanti. It seems like it should be reasonably st…
kdm9 updated
9 months ago
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Hi there,
Sorry if it might be a stupid question. I just wonder what is the difference between qcovs from NCBI blast and qcovhsp from diamond blast? What I am doing now basically is to blastp of tr…
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Per conversation in MAD session today, there are problems with installation instructions that need to be fixed:
http://eel-pond.readthedocs.io/en/latest/0-install-aws.html
and
http://eel-pond…
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Hi there,
Should I specify an evalue for the hmmscan for Including homology searches as ORF retention criteria? In the tutorial, you didn't specify a evalue: `hmmsearch --cpu 8 --domtblout pfam.dom…
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Hi!
I just tried to reinstall the databases which fails in the step
```
curl -o aa_seq_euk.fasta.gz ftp://cegg.unige.ch/OrthoDB8/Eukaryotes/FASTA/aa_seq_euk.fasta.gz
curl: (28) Failed to conn…
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Hi,
When I use EVM to integrate gene prediction, I encounter some genes without a start codon and/or stop codon. But I have used '--stop_codons TAA,TGA,TAG' parameters.
PASA, Cufflinks, Stringtie …
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I have run two trinity assemblies through the TransDecoder pipeline and was surprised to find that in one case the exact same number of transcripts was found whether or not I included the blast and hm…
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Would be great if we can list the software or bioinformatic pipelines required for de novo RNAseq analysis.
Pipeline to add:
- [x] FastQC
- [x] MultiQC
- [x] [Trimmomatic](https://bioconda.git…
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Hello, I'm sorry if I made any mistakes. I try now to run sequence analyses and in the console after code is entered, it happenes absolutely nothing, via nohup no any log file whatsoever and I don't s…