User: Vanilla
Vanilla • 50
- Reputation:
- 50
- Status:
- New User
- Location:
- Hong Kong
- Last seen:
- 6 months, 3 weeks ago
- Joined:
- 2 years, 9 months ago
- Email:
- y********@gmail.com
Posts by Vanilla
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... Got it. Thanks Santosh! ...
written 7 months ago by
Vanilla • 50
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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 7 months ago by
Vanilla • 50
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... Thanks Santosh! Would DESeq2 accept FPKM values as input? Or only raw read count? ...
written 7 months ago by
Vanilla • 50
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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 7 months ago by
Vanilla • 50
• updated
7 months ago by
Santosh Anand • 3.8k
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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 14 months ago by
Vanilla • 50
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... Got it. Thanks very much for your help Devon! ...
written 14 months ago by
Vanilla • 50
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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 14 months ago by
Vanilla • 50
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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 14 months ago by
Vanilla • 50
• updated
14 months ago by
Devon Ryan ♦ 82k
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... Hi all:
I recently got quite confused with two SAM flags got from BWA alignment, which is "**supplementary alignment**" from chimeric alignments and "**not primary alignment**" (or "secondary alignment") from multiple mapping.
**What samtools explain about these two flags is:**
(Refer to https://s ...
written 14 months ago by
Vanilla • 50
• updated
14 months ago by
Devon Ryan ♦ 82k
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... Hi Igor,
Thanks very much for your answer. Actually their explanation is still vague, and I still didn't get how this score can reflect how strong the peak is.
But anyway, as they suggested using column7-9 for downstream, I may only take this score for visualization but not used for filtering.
Th ...
written 23 months ago by
Vanilla • 50
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