Output of AssemblePairs.py sequential and align is the same

[Yanting Hee]

I have R1 and R2 of 250bp length each and hence majority of the paired reads would not overlap. Thus I thought of doing sequential assembly, however I noticed only ~30% of reads successfully assembles. Comparing with the output of AssemblePairs.py align, both results in the same number of reads being successfully assembled. Suspect this is a bug?

I performed STAR mapping of my R1 and R2 and confirmed that reads that have failed assembly either have overlap less than the minlen, or no overlap. Regardless these reads do map to the TCR genes and thus should assemble via reference assembly, if I understand correctly?

[ssnn]

Would it be possible for you to email example data (input sequences and reference) and the command you used to [e-mail], please? I would like to reproduce the issue to check if there is a bug or some parameters need to be adjusted.

[Yanting Hee]

Apologies this is due to user error, as I parsed read1 and read2 wrongly into the -1 and -2 options. Fixed it and ~80% of the reads now passes assembly. So sorry about the false alarm.

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[ssnn]

Awesome! No worries about false alarms. It is common to require a few tries to get “the perfect” command.