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Read Assembly and Annotation Pipeline Tool
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Paired end reads #7

Closed rfcohen closed 3 years ago

rfcohen commented 3 years ago

How to feed paired end reads into RAPT? It's not clear from he documentation how one feeds paired end reads into RAPT.

Thanks.

thibaudnis commented 3 years ago

You can provide a file of paired-end reads, with the two reads of a pair adjacent to each other in the file (i.e. spot 1 fwd, spot 1 rev, spot 2 fwd, spot 2 rev) . We will add this to the doc shortly. Thanks for pointing out the omission.

rfcohen commented 3 years ago

Thank you. But actually I want to provide two files, R1 and R2 separately.

-Rob

On Dec 11, 2020, at 4:56 PM, Francoise Thibaud-Nissen notifications@github.com wrote:

 You can provide a file of paired-end reads, with the two reads of a pair adjacent to each other in the file (i.e. spot 1 fwd, spot 1 rev, spot 2 fwd, spot 2 rev) . We will add this to the doc shortly. Thanks for pointing out the omission.

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thibaudnis commented 3 years ago

This is not currently supported.

rfcohen commented 3 years ago

Looks like SKESA supports it. Also SKESA supports inputting Gzip’d files which would be nice, or at least documented that RAPT does accept compressed files.

Thanks.

-Rob

On Dec 11, 2020, at 4:59 PM, Francoise Thibaud-Nissen notifications@github.com wrote:

 This is not currently supported.

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thibaudnis commented 3 years ago

Yep, thanks for the suggestions!

buihoangphuc412 commented 3 years ago

I have 2 files: R1 and R2, I seem like RAPT did not support ./run_rapt_gcp.sh submitfastq gs://buihoangphuc412/VN0211-s_1_1_sequence.qf.fastq.gz gs://buihoangphuc412/VN0211-s_1_2_sequence.qf.fastq.gz -b gs://buihoangphuc412/VN0211 --organism "Helicobacter pylori" --strain "VN0211"

thibaudnis commented 3 years ago

Okay, I see we need to start accepting R1 and R2. In the meantime, there seems to be a number of options out there for combining the two files: interleave-fastq, or reformat.sh in the BBmap suite that may help.

thibaudnis commented 3 years ago

@buihoangphuc412 and @rfcohen: starting with v0.3.0, you can now provide the forward and reverse reads of a run in separate files, and these files can be gzipped. This version of RAPT is also much faster. See announcement for this new release: https://ncbiinsights.ncbi.nlm.nih.gov/2021/02/12/rapt-release/ . Thanks for your feedback!