Mustafa Elshani
Mustafa Elshani
Hi @rob-p I have very similar issue in lowly mapped rated with salmon quant alignment based, 30-35%. The RNA is derived from FFPE human tissue so as expected it is...
This seem to have solved it https://github.com/likelet/LncPipe/pull/55/commits/c39867c7dacb5e8c24442d6b9b6cc05e59a1d587
Does anyone have an answer to this, are those error models 'safe' to ignore?
Thank @rob-p and @gmarcais, that clarifies it. There's only a handful of reads that seem to fall in this category. Just a suggestion would it better to have just a...
I think this was first asked back in 2009 in forums, any update or workaround on how to implement it?
Getting the very same error, anyone managed to fix it?
Hi Mike Updated both tximeta and bio-conductor however still got the message `importing quantifications reading in files with read_tsv 1 2 3 4 5 6 7 8 couldn't find matching...
I think my issue is that I am using the alignment-based mode (which I require) in salmon and this does not have the `"index":"/path/to/genecode.v35_salmon_1.3.0"` metadata in` cmd_info.json` file of counts,...
How would you go about getting the checksum of the source file. The file I used on `- t` on salmon quant was downloaded from GENCODE ftp, however this does...
Apologies in delay in replying yes running `salmon index` on the same reference does indeed have the same hash. and so does the fasta digest . Just wondering in salmon...