search

masai1116 / SHARE-seq-alignmentV2

Pipeline for demultiplexing and aligning both ATAC and RNA data generated in SHARE-seqV2
GNU General Public License v3.0
11 stars 7 forks source link

'Illumina 300 cycle' sequencing strategy #7

Open Rui-Jing opened 1 year ago

Rui-Jing commented 1 year ago

Hi Sai: Thanks for sharing these scripts. 

     I did some tests with the SHARE-seq technique, which selected the illuminat 300cycles sequencing strategy, and everything else was based on your 2020 Cell paper.  

     My question is what parameters should I modify to enable the data to be analyzed normally for the double-paired 150bp sequencing strategy.

      Thanks for your help.

Sincerely,

Rui

masai1116 commented 1 year ago

Hi Rui,If you are talking about using 15088*150 configurations for sequencing, this won’t work because it will not cover the entire index 1. There have to be 99bp index 1.Best,SaiOn Feb 15, 2023, at 12:33 AM, Rui-Jing @.***> wrote: Hi Sai: Thanks for sharing these scripts. I did some tests with the SHARE-seq technique, which selected the illuminat 300cycles sequencing strategy, and everything else was based on your 2020 Cell paper. 

 My question is what parameters should I modify to enable the data to be analyzed normally for the double-paired 150bp sequencing strategy.

  Thanks for your help.

Sincerely, Rui

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>

Rui-Jing commented 1 year ago

Hi Sai: Thanks for receiving your reply. I wasn't quite right with that description. I have obtained the data using the sequencing strategy of 100998*100 (300 cycle total), but I don't know how to analyze the data with the SHARE-seq-alignmentV2. What parameters should I modify to enable me to do the analysis pipeline. I sincerely hope to get your help.

Rui-Jing commented 1 year ago

(100bp99bp8bp*100bp) equal to (Read1 Index1 Index2 Read2)

masai1116 commented 1 year ago

In this case, you don’t need to change the script at all. It should be compatible.On Feb 15, 2023, at 10:06 AM, Rui-Jing @.**> wrote: Hi Sai: Thanks for receiving your reply. I wasn't quite right with that description. I have obtained the data using the sequencing strategy of 100998100 (300 cycle total), but I don't know how to analyze the data with the SHARE-seq-alignmentV2. What parameters should I modify to enable me to do the analysis pipeline. I sincerely hope to get your help.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you commented.Message ID: @.***>

Rui-Jing commented 1 year ago

Thanks. I got it.