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bcgsc / RNA-Bloom

:hibiscus: reference-free transcriptome assembly for short and long reads
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Correct Strand Information and Pairing #7

Closed sum732 closed 4 years ago

sum732 commented 4 years ago

Hi Ka Ming,

The strandedness confuses me ( and hopefully others), so just to get this part right. I have Illumina PE which is stranded and PacBio Long reads, which are not stranded.

Now typically before alignments and processing I consult the following to ensure I am giving the right orientation " https://github.com/igordot/genomics/blob/master/notes/rna-seq-strand.md" The reverse option is true for a typical dUTP ( Illumina TruSeq or NEB etc).

In the detailed README you have mentioned that: -left /path/to/reads_2.fastq -right /path/to/reads_1.fastq

So the order you have mentioned above for left (R2) and right (r1) refers to the reverse as above mentioned? Thanks!!

kmnip commented 4 years ago

Yes, you are correct. The _2 reads are the "left" reads and they are in the forward orientation, whereas the _1 reads are the "right" reads and they are in the reverse orientation.