User: afli

gravatar for afli
afli140
Reputation:
140
Status:
Trusted
Location:
China, Beijing, IGDB
Last seen:
8 hours ago
Joined:
4 months, 1 week ago
Email:
a***@genetics.ac.cn

Posts by afli

<prev • 105 results • page 1 of 11 • next >
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Comment: C: Too few differentially expressed genes identified by edgeR
... Thank you for your suggestion RamRS, I give the data link and paste the scripts so that everyone can download this data (small size), and run this in edgeR, totally need about 2 minutes. And I edit my post with more detail for those who do not have much time to run and check my data. Hope this is OK ...
written 8 hours ago by afli140
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Too few differentially expressed genes identified by edgeR
... Dear all, I'm new in using edgeR. I get no diffrentially expressed genes and I don't know why, could anyone give me some advice? Thank you very much! I pasted the data link and my scripts as follows. data link: https://de.cyverse.org/dl/d/5F987820-8F84-4772-8561-416202A11580/allh.counts_test.txt ...
edger written 9 hours ago by afli140
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Comment: C: Software to visualize ChIP-seq peak file
... Thank you for your contribution! ...
written 2 days ago by afli140
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Comment: C: Software to visualize ChIP-seq peak file
... Yeah, this is a very good idea! I checked this and get the expected pdf file. Thank you! ...
written 2 days ago by afli140
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Software to visualize ChIP-seq peak file
... Dear all, I have bam or bigwig files from ChIP-seq data. IGV is a good tool to visualizing them, but there is some error when opening the saved svg file in adobe illustrator, so I cannot do modification and get the expected beautiful figures. Is there any other software that can visualize these file ...
chip-seq visualization written 2 days ago by afli140
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Comment: C: Filter VCF with bash commands
... Never mind. If so, you can add another '?' : `perl -ne 'print $_ if /;?QD=(-?\d+(\.\d+)?)/ && $1>8' test.txt |less -S` It is just a solution for simple data as supplied in the post, with more complex data, we can do some modification of this, or use other better methods as below. ...
written 10 days ago by afli140
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Comment: C: Filter VCF with bash commands
... OK, let's modify this further: `perl -ne 'print $_ if /;QD=(-?\d+(\.\d+)?)/ && $1>8' test.txt |less -S` ...
written 10 days ago by afli140
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Comment: C: Filter VCF with bash commands
... Sorry, but this is easy to solve. `perl -ne 'print $_ if /QD=(\d+(\.\d+)?)/ && $1>8' test.txt |less -S` ...
written 10 days ago by afli140
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Comment: C: Filter VCF with bash commands
... Hi, try this line; `perl -ne 'print $_ if /QD=(\d+)/ && $1>8' test.txt |less -S` ...
written 10 days ago by afli140 • updated 10 days ago by finswimmer6.9k
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Comment: C: Seemingly contradictory ATAC-seq conclusions from a Science journal paper?
... Maybe they mean the generation of TF binding site make chromatin more accessible near the binding sites. If there is a week binding site, then in this site the chromatin is generally not very accessible, when the site is strong for TF binding, then in this site the chromatin may be opened by the loa ...
written 10 days ago by afli140

Latest awards to afli

Centurion 10 days ago, created 100 posts.
Scholar 14 days ago, created an answer that has been accepted. For C: DEseq2 logfold interpretation
Scholar 19 days ago, created an answer that has been accepted. For C: DEseq2 logfold interpretation
Scholar 24 days ago, created an answer that has been accepted. For A: Compare expression of one group to the mean of others using DESeq2
Teacher 24 days ago, created an answer with at least 3 up-votes. For C: DEseq2 logfold interpretation
Scholar 25 days ago, created an answer that has been accepted. For A: Compare expression of one group to the mean of others using DESeq2
Rising Star 8 weeks ago, created 50 posts within first three months of joining.

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