Michael Love

The Gencode + decoy hash was going to break plans on integrating with GA4GH to support all txomes (as the hash value on the server side wouldn't include the decoy...

This thread made me realize, the above workaround would be a useful technique to preserve the reference hash value when users want to add non-reference transcripts. For example, sometimes users...

Thanks for feedback @jtheorell So we don't have this working yet, but my thoughts were that we could have Salmon distinguish between the "primary" reference sequences of interest (e.g. transcripts),...

This is a perfectly valid solution. I’m not sure if the target file would have the same hash as the transcripts from the source. Can you check for your example?...

You could run `salmon index` on the file and then look into the directory that is created to find the hash. The lightweight version is to run `compute_fasta_digest` which can...

Let me ask @rob-p, is it possible to have an option to index the target file as part of quant? Indexing is fairly fast, and then reads quantified with the...

Thanks @mbergins

What is your ``` packageVersion("tximeta") ``` Your first place to check is the NEWS file. If you have a version less than when it was added, then your local version...

``` URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_38/gencode.v38.annotation.gtf.gz': Timeout of 60 seconds was reached ``` This means that your connection was too slow to download this resource from EBI. Is it possible for you to...

Hi @pkerrwall If you see my comment from 9/4/2020: https://github.com/mikelove/tximeta/issues/38#issuecomment-687100040 ...I don't think you have a seqhash in the quantification metadata files in alignment mode (there is no transcriptome to...