User: Houyu Zhang

gravatar for Houyu Zhang
Houyu Zhang20
Reputation:
20
Status:
New User
Location:
China/Guangzhou
Last seen:
3 days, 5 hours ago
Joined:
3 years, 2 months ago
Email:
h*********@gmail.com

Posts by Houyu Zhang

<prev • 31 results • page 1 of 4 • next >
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Answer: A: Generating genesets matched for GC content and length
... Do you mean the generated dataset must be genes? If so, consider the gene length differs, you can try to use [this script][1] for your purpose with little modification because your sequence pool is limited to genes. [1]: https://github.com/HouyuZhang/Pieces_of_tools/blob/master/Negetive_sequen ...
written 5 weeks ago by Houyu Zhang20
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Answer: A: How to generate random genomic sequences that are GC- and length-matched to my i
... I wrote a pure bash script for this purpose, verbose but useful. Wish to see better versions :) [Negetive_sequence_matched_length_GC.sh][1] This script is for generating length and GC content matched background sequence, heavily using bedtools Negetive_sequence_matched_length_GC.sh [input ...
written 5 weeks ago by Houyu Zhang20
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measure the distribution bias in genomic features
... Hi everyone, I'm recently analyzing DNA methylation data and facing an obstacle problem here: As we know that the DNA methylation distribution can vary differently in genomic features (core promoter, enhancer, CpGIsland, etc). I want to measure the distribution bias among these genomic feature ...
statisticas written 8 months ago by Houyu Zhang20 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: A question on MEME results
... Hi Mensur, I have followed your suggestions using `-pal` and got a reasonable result below: sampled results: I have also tried different -mod parameters including `anr`, but results are all weird except for `-mod zoops`, so, I may use this later. Thanks for your kind help! ...
written 13 months ago by Houyu Zhang20
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Comment: C: A question on MEME results
... Thank you again Mensur, I will try your advice and show the result later :) ...
written 13 months ago by Houyu Zhang20
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Comment: C: BagFoot TF foot printing
... Hi Ravi, I have sucessfully used this package before and I may give you some suggestions. The default result of bagfoot is without p-value / q-value, however, the code for statistical analysis exists in original bagfoot code. Just use `gen_bagplot_chisq()` instead of `gen_bagplot()` ....... ...
written 14 months ago by Houyu Zhang20
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Comment: C: BagFoot TF foot printing
... Hi rbronste, I have managed it to work recently after painful 5 days on debugging, I noticed this post is 15 months ago, So, if you still need some help, please email me at `hughiez047@gmail.com` and I will provide you my detailed records :-) Hope this helps, best wishes! ...
written 18 months ago by Houyu Zhang20
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Comment: C: BagFoot TF foot printing
... I have fine-tune the index file to fit .meme file and it works fine :-) ...
written 18 months ago by Houyu Zhang20
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Comment: C: BagFoot TF foot printing
... It' s due to replicted columns of pooled hotspot file and need some alteration on this file to get it work :-) ...
written 18 months ago by Houyu Zhang20
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Comment: C: BagFoot TF foot printing
... I have re-ranked my index file to fit .meme file and got normal result, Thank you! ...
written 18 months ago by Houyu Zhang20

Latest awards to Houyu Zhang

Popular Question 12 months ago, created a question with more than 1,000 views. For Split fastq according to barcodes
Supporter 20 months ago, voted at least 25 times.

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