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YiPeng-Gao / scDaPars

Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
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how to generate raw PDUI #1

Closed BenxiaHu closed 3 years ago

BenxiaHu commented 3 years ago

Hello, I want to run scDaPars to analyze scRNA-seq. scDaPars takes as input the raw PDUI generated by DaPars2. Would you like to tell me how to run DaPars2? I have checked the DaPars2 (https://github.com/3UTR/DaPars2), it does not show how to run it. Best,

YiPeng-Gao commented 3 years ago

Hi, Thanks for your interest in scDaPars. Please view the attached website for detailed instructions for generating raw PDUI.

http://lilab.research.bcm.edu/dldcc-web/lilab/Lei/DaPars2_Documentation/DaPars2.html

Hope this helps!

Hello, I want to run scDaPars to analyze scRNA-seq. scDaPars takes as input the raw PDUI generated by DaPars2. Would you like to tell me how to run DaPars2? I have checked the DaPars2 (https://github.com/3UTR/DaPars2), it does not show how to run it. Best,

learner-bioinformation commented 3 years ago

Hello, I want to run scDaPars to analyze scRNA-seq. scDaPars takes as input the raw PDUI generated by DaPars2. Would you like to tell me how to run DaPars2? I have checked the DaPars2 (https://github.com/3UTR/DaPars2), it does not show how to run it. Best, Hi, has the problem of generating the raw PDUI been solved? Can you open the website http://lilab.research.bcm.edu/dldcc-web/lilab/Lei/DaPars2_Documentation/DaPars2.html? How did you generate the raw PDUI? Best,

YiPeng-Gao commented 3 years ago

Sorry, Please check the website https://leilisysbio.github.io/DaPars2_Documentation/DaPars2.html. I will also update the github page with the pipeline for scDaPars.

Hope this will help!

learner-bioinformation commented 3 years ago

Hi, is there a test file? I don’t know how the file "sequencing_depth_file=mapping_bam_location_with_depth.txt" is generated? Best,

YiPeng-Gao commented 3 years ago

We will update the GitHub page for DaPars2 shortly with test files. Thanks for the reminder!

learner-bioinformation commented 3 years ago

hi, how do I get the sequencing depth file? I found that the sequencing depth file (mapping_bam_location_with_depth.txt) cannot be generated with bedtools. Best.

YiPeng-Gao commented 3 years ago

hi, how do I get the sequencing depth file? I found that the sequencing depth file (mapping_bam_location_with_depth.txt) cannot be generated with bedtools. Best.

Hi, you can use "samtools flagstat bam_file > flagstat.txt" to get the sequencing depth for each sample, and then compile into one txt file formatted as "mapping_bam_location_with_depth.txt".

learner-bioinformation commented 3 years ago

Thanks, i will try.

------------------ 原始邮件 ------------------ 发件人: "YiPeng-Gao/scDaPars" @.>; 发送时间: 2021年5月17日(星期一) 凌晨0:29 @.>; @.**@.>; 主题: Re: [YiPeng-Gao/scDaPars] how to generate raw PDUI (#1)

hi, how do I get the sequencing depth file? I found that the sequencing depth file (mapping_bam_location_with_depth.txt) cannot be generated with bedtools. Best.

Hi, you can use "samtools flagstat bam_file > flagstat.txt" to get the sequencing depth for each sample, and then compile into one txt file formatted as "mapping_bam_location_with_depth.txt".

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learner-bioinformation commented 3 years ago

Hi, I would like to ask if it is the hg38 file for cellranger align, can the UCSC hg19 bed file (the test set given by dapars2) be used in step 1 of dapars2? Best,

YiPeng-Gao commented 3 years ago

Hi, I would like to ask if it is the hg38 file for cellranger align, can the UCSC hg19 bed file (the test set given by dapars2) be used in step 1 of dapars2? Best,

I would suggest you generate a hg38 bed file for that.

ghost commented 3 years ago

"samtools flagstat bam_file > flagstat.txt " Which value is used in the result file for subsequent analysis 85207970 + 0 in total (QC-passed reads + QC-failed reads) 5350668 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 73549948 + 0 mapped (86.32% : N/A) 79857302 + 0 paired in sequencing 39928651 + 0 read1 39928651 + 0 read2 62977510 + 0 properly paired (78.86% : N/A) 63902424 + 0 with itself and mate mapped 4296856 + 0 singletons (5.38% : N/A) 173078 + 0 with mate mapped to a different chr 127302 + 0 with mate mapped to a different chr (mapQ>=5)

YiPeng-Gao commented 3 years ago

"samtools flagstat bam_file > flagstat.txt " Which value is used in the result file for subsequent analysis 85207970 + 0 in total (QC-passed reads + QC-failed reads) 5350668 + 0 secondary 0 + 0 supplementary 0 + 0 duplicates 73549948 + 0 mapped (86.32% : N/A) 79857302 + 0 paired in sequencing 39928651 + 0 read1 39928651 + 0 read2 62977510 + 0 properly paired (78.86% : N/A) 63902424 + 0 with itself and mate mapped 4296856 + 0 singletons (5.38% : N/A) 173078 + 0 with mate mapped to a different chr 127302 + 0 with mate mapped to a different chr (mapQ>=5)

I would recommend use the number of mapped reads. In your case, that is "73549948".