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yanboANU / Kmer2SNP

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How to run with PE reads? #2

Closed ghost closed 4 years ago

ghost commented 4 years ago

Hello,

how should it be run with PE reads? thanks

yanboANU commented 4 years ago

Hi,

If there are more than 2 input fastq file,

sh runkmercalling.sh 31 60 single_chr22_60x_p1_data.fq,single_chr22_60x_p2_data.fq

ghost commented 4 years ago

thanks,

would it actually make sense to juste use the R1 reads? As often the R2 reads in illumina sequencing are of lower quality

yanboANU commented 4 years ago

If your coverage is enough, just use R1 reads is ok I think. I never heard that R2 reads in illumina are of lower quality.

在 2020年7月30日，下午7:37，aderzelle notifications@github.com 写道：



thanks,

would it actually make sense to juste use the R1 reads? Are often the R2 reads in illumina sequencing are of lower quality

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/yanboANU/Kmer2SNP/issues/2#issuecomment-666313244, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHZV5JQTSZYEMJPRWIVVL4TR6FLORANCNFSM4PLZV2XQ.

ghost commented 4 years ago

Oh for example: Quality-profiles-for-R1-and-R2-reads-the-boxplots-in-the-first-column-display-the

This comes from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381044/

So Kmer2SNP does not use paired information right? It is indifferent if the reads are paired or not for it to run?

yanboANU commented 4 years ago

Yes, Kmer2SNP does not use paired information.

Yanbo Li 4.32, Building 145 (Hanna Neumann) Research School of Computer Science The Australian National University

Email: yanbo.li@anu.edu.aumailto:yu.lin@anu.edu.au

From: aderzelle notifications@github.com Sent: Friday, July 31, 2020 3:24 AM To: yanboANU/Kmer2SNP Kmer2SNP@noreply.github.com Cc: Yanbo Li yanbo.li@anu.edu.au; Comment comment@noreply.github.com Subject: Re: [yanboANU/Kmer2SNP] How to run with PE reads? (#2)

Oh for example: [Quality-profiles-for-R1-and-R2-reads-the-boxplots-in-the-first-column-display-the]https://user-images.githubusercontent.com/23341393/88954010-0510b900-d29a-11ea-8c99-5382bd42e14c.png

This comes from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381044/

So Kmer2SNP does not use paired information right? It is indifferent if the reads are paired or not for it to run?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/yanboANU/Kmer2SNP/issues/2#issuecomment-666542579, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AHZV5JR7F4TSYK5EW6O7HC3R6GUD5ANCNFSM4PLZV2XQ.

ghost commented 4 years ago

cool thanks