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masai1116 / SHARE-seq-alignmentV2

Pipeline for demultiplexing and aligning both ATAC and RNA data generated in SHARE-seqV2
GNU General Public License v3.0
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'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

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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.

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Rui-Jing commented 1 year ago

Thanks. I got it.