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Zhiliang-Bai / Patho-DBiT

Patho-DBiT is a platform to spatially decode RNA Biology in archival FFPE tissues.
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How to produce RV=$tmp/${sample}_R1_filtered.final.fastq.gz #1

Open xieduo7 opened 1 month ago

xieduo7 commented 1 month ago

Hi @Zhiliang-Bai ,

Thanks for your code.

I am wondering how to generate RV=$tmp/${sample}_R1_filtered.final.fastq.gz from raw reads before running st_pipeline_run.py. Trimming read 1 with Cutadapt? I was confused because I saw thatst_pipeline_run.py can also trim the reads.

Thank you!

Best, Duo

Sina-soton commented 5 days ago

I am also stuck at the same point. Would greatly appreciate any advice!

Best wishes Sina

Zhiliang-Bai commented 4 days ago

Hi Duo and Sina,

The raw data I uploaded to GEO has already been filtered, with the R1 file for each sample ready to be used as input for the st_pipeline. However, the GEO team has requested the upload of the original, untrimmed raw data, and I am currently working on addressing this request.

Best, Zhiliang

xieduo7 commented 4 days ago

Hi Dr.@Zhiliang-Bai ,

Thanks for your reply.

I think we still need to trim the TSO primer (AAGCAGTGGTATCAACGCAGAGTGAATrGrG+G, denoted in sup table3) as in 10X pipeline before running st_pipeline? Because I saw lots of TSO primers in the GEO R1:

image

st_pipeline doesn't include this trimming. So if we don't trim these TSO primers, it will lead to a lot of mismatchs and may cause these reads cannot be mapped to the reference genome.

Did you do this before running st_pipeline?

Thank you!

Best, Duo

Sina-soton commented 1 day ago

Hi Zhiliang and Duo

Thank you very much for your reply Zhiliang.

I agree with Duo, are there any specific trimming requirements needed before alignment? I am having trouble getting any significant mapping of the read 1 transcripts to the reference genome.

Best wishes Sina