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blahah / transrate

Understand your transcriptome assembly
http://hibberdlab.com/transrate
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interleaved reads #162

Open macmanes opened 9 years ago

macmanes commented 9 years ago

Can we have an option of inputting interleaved reads, like from khmer/seqtk? Not sure if SNAP/salmon can handle this..

transrate --assembly bwa.Trinity.fasta --interleaved Schizo.50M.interleaved.fq.gz --threads 16
rob-p commented 9 years ago

Hi @macmanes,

It looks like SNAP has some code for this, but I'm not sure how well tested it is. However, assuming that SNAP handles it and generates a valid BAM, Salmon is indifferent on how the raw reads were provided to the aligner. That is, Transrate talks to Salmon only through BAM, so if SNAP handles it, it Salmon should be fine.

macmanes commented 9 years ago

OK - cool!

blahah commented 9 years ago

Yeah SNAP can handle it, so we just need to add it to the Transrate interface. How about if left and right are the same file, assume interleaved? I'd prefer to avoid adding another argument.

macmanes commented 9 years ago

might be asking for trouble with a non-standard CLI option.. I do get your point about not adding more options tho..

blahah commented 9 years ago

Interleaving is non-standard IMO (grumble grumble...). Are you thinking that the 'standard' would be to have a third argument, --interleaved or something similar?

macmanes commented 9 years ago

yes, --interleaved is what I was thinking about.

ctb commented 9 years ago

+1

Interleaved supports streaming :>

ctb commented 9 years ago

(What the heck does "non-standard" mean in this field, anyway?)

blahah commented 9 years ago

Just that very few tools use it. khmer is the only thing I use frequently that does I think. But, users are in charge, so we'll add it :)