User: Vanilla
Vanilla • 80
- Reputation:
- 80
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- Hong Kong
- Last seen:
- 6 months, 3 weeks ago
- Joined:
- 3 years, 6 months ago
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Posts by Vanilla
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... For the question "how does `macs2` generate the `b3tTime0_control_lambda.bdg`", I found the answer here: https://groups.google.com/forum/#!msg/macs-announcement/9N-sMFc8784/SxlSU8joSkwJ.
In brief, MACS2 estimates control lambda from the ChIP sample itself when the control sample is absent. ...
written 7 months ago by
Vanilla • 80
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... Now the`'possible_controls'` has been changed to `'Controlled by'`. ...
written 8 months ago by
Vanilla • 80
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... Got it. Thanks Santosh! ...
written 16 months ago by
Vanilla • 80
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... What if I only have FPKM values? Could I take log of them and remove low expressed genes (to make the distribution approximate to normal)? ...
written 16 months ago by
Vanilla • 80
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... Thanks Santosh! Would DESeq2 accept FPKM values as input? Or only raw read count? ...
written 16 months ago by
Vanilla • 80
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... Hi all!
I'm going to detect differentially expressed genes with RNA-seq data got from some "GFP positive cells" and "GFP negative cells". However, the cDNA are sequenced with two different methods, one as "normal" RNA-seq, and the other is low-input RNA-seq (only requires a small amount of starting ...
written 16 months ago by
Vanilla • 80
• updated
16 months ago by
Santosh Anand ♦ 4.7k
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... Hi all!
I got several ATAC-seq and ChIP-seq samples, but unfortunately, some of them are with low sequencing depth after I trimmed the reads with mapping quality, duplicates, and mitochondrial DNA and keep proper paired (it's paired end reads). Only a few peaks can be called for them and it's hard ...
written 23 months ago by
Vanilla • 80
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... Got it. Thanks very much for your help Devon! ...
written 23 months ago by
Vanilla • 80
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... Got it. So I will also just throw them away.
In case you also have secondary alignments from multiple mapping(e.g. due to repeat sequences), should them also be discarded for ChIP-seq analysis? I'm also curious why I didn't get any of secondary alignments. ...
written 23 months ago by
Vanilla • 80
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... Thanks Devon!
I agree as just checked that this is a repeat "ACACACATATACACAGTGCTAAGTTCATTGT" around chr6:144444722 on mm10, which causes the multiple alignments for the reads.
Oh I also have a lot of cases with supplementary alignments mapped elsewhere, with sequence overlaps but not genome coor ...
written 23 months ago by
Vanilla • 80
• updated
23 months ago by
Devon Ryan ♦ 90k
Latest awards to Vanilla
Appreciated
8 months ago,
created a post with more than 5 votes.
For Difference between chimeric alignments and multiple mapping
Good Question
8 months ago,
asked a question that was upvoted at least 5 times.
For Difference between chimeric alignments and multiple mapping
Popular Question
16 months ago,
created a question with more than 1,000 views.
For How is "integer score for display" calculated in MACS2
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Difference between chimeric alignments and multiple mapping
Popular Question
16 months ago,
created a question with more than 1,000 views.
For genomeCoverageBed for paired end reads
Student
16 months ago,
asked a question with at least 3 up-votes.
For Difference between chimeric alignments and multiple mapping
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