Read length distributon after processing

[coolmak32]

Hello, I have using afterqc with default settings to remove adapter sequences from RNA Seq read files. My original files have all the reads of uniform length. After processing with afterqc the sequence lengths are not uniform. Therefore, I have two questions 1) Can I somehow make all the reads of uniform length? 2) What implications are we talking if the length in not uniform down the analysis (Original read length for all reads was 151 bases, after afterqc read length is between 35-142).

[sfchen]

I suggest you to use our new tool fastp (https://github.com/OpenGene/fastp) to address this issue. With fastp, you can control the output with much more configurable options.

And fastp is much much faster than AfterQC (10X)

[coolmak32]

I used afterqc for half of my experiments therefore thats not the option at this point.

On Fri, Mar 9, 2018 at 2:50 AM Shifu Chen ***@***.***> wrote: I suggest you to use our new tool fastp (https://github.com/OpenGene/fastp) to address this issue. With fastp, you can control the output with much more configurable options. And fastp is much much faster than AfterQC (10X) — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#35 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Afd3lgAuzuX6X7RQWWv0tfkLwS2OaEecks5tcjQrgaJpZM4Sj1Kr> .

-- Kuldeep Makwana (Ph.D. candidate regulatory biology) SR 271,BGES Cleveland State University. 216-262-9156

[sfchen]

AfterQC performs automatic adapter trimming, and this is why it causes non-uniform read length.

[sfchen]

Adapters should be trimmed before downstream analysis. So AfterQC does it automatically.

Would you like an option to disable adapter trimming?

[coolmak32]

I aligned my previous data after using Afterqc and everything went well. I was just wondering if is it a big concern to have non uniform length distribution. I understand after adapter trimming it is often may be difficult to have all the reads of same length.

On Fri, Mar 9, 2018 at 3:00 AM Shifu Chen ***@***.***> wrote: AfterQC performs automatic adapter trimming, and this is why it causes non-uniform read length. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#35 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Afd3lsor4n0uGR6V-viYP1LM3o8yGvhhks5tcjargaJpZM4Sj1Kr> .

-- Kuldeep Makwana (Ph.D. candidate regulatory biology) SR 271,BGES Cleveland State University. 216-262-9156

[sfchen]

No, don't worry, non-uniform length distribution is never a problem.

[coolmak32]

Thanks.

On Fri, Mar 9, 2018 at 3:49 AM Shifu Chen ***@***.***> wrote: No, don't worry, non-uniform length distribution is never a problem. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#35 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/Afd3lgpXuYHbRG5HaIhZE8_r9n7IIR6rks5tckICgaJpZM4Sj1Kr> .

-- Kuldeep Makwana (Ph.D. candidate regulatory biology) SR 271,BGES Cleveland State University. 216-262-9156