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bsmith030465
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Michael Dondrup
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I0110
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Recent Replies
Comment: Split fasta based on symbol and numeric position in header
by
GenoMax
100k
You may be able to do
$ cut -d "+" -f1 your_file.fa
>NZ_LR732827.1_2243__GH81(350-867)
WGDWNVSWRMPQDGPGGQYMDVTSVQGSPY
Comment: Is Biopython a Package or Library?
by
Ram
32k
If we were to rename the py file to `Seq2.py`, would the import statement change to `from Bio.Seq2 import Seq`?
Comment: Split fasta based on symbol and numeric position in header
by
heskett
•
0
I don't know if this will be helpful, but in my years of experience with human genomics, I've only seen FASTA files as storage of raw seque…
Comment: Synonymous and asynonymous sites in Ka/Ks
by
Istvan Albert
87k
to be honest your question is a bit confusing, first you say
> not very much interested on how they are calculated
but then you seem to w…
Comment: Can too high of a ChIPQC RiP% be indicative of insufficient stringency in peak c
by
jared.andrews07
9.3k
As you said, it's going to vary, but I'd say the average H3K27ac peak is probably 1-5kb in size. If you're getting lots of peaks that are 1…
Comment: Clustering of short peptide sequences
by
xiaoyuzhangh
•
0
Thanks a lot! I can't run the Clustal Omega.
[nbp-25-183-57:~] xiaoyuzhang% /Users/xiaoyuzhang/Hammock_v_1.2.0/clustal-omega-1.2.0/clusta…
Answer: Is Biopython a Package or Library?
by
Istvan Albert
87k
"Library" is a generic term that describes a type of software that you make use of within your programs rather than running the software al…
Comment: Can too high of a ChIPQC RiP% be indicative of insufficient stringency in peak c
by
gkunz
▴
10
Hi Jared,
Thank you for the thoughtful response! This is the second time you have provided a clear and helpful answer to a question i …
Answer: Genes with identical reads mapping values across all samples - Kallisto
by
Michael Dondrup
48k
If the transcripts are of fully identical sequence there is no informmation that could help to distinguish them for Kallisto, so in a sense…
Comment: How to get output of annotated genes from ChIPseeker tool
by
Sam
▴
160
Your question is unclear, but take a look at ```addFlankGeneInfo``` parameter
Answer: Can too high of a ChIPQC RiP% be indicative of insufficient stringency in peak c
by
jared.andrews07
9.3k
This is going to depend very much on the protein being immunoprecipitated. These ranges are not outside the norm for histone marks - I've s…
Comment: protein-protein interaction analysis
by
au.rinki.bio
▴
10
Thank You so much. Nicely explained
Comment: R libraries to match SNPs by positions (including switching and flipping)
by
Ram
32k
I'm not sure if this is a common requirement - packages/functions may not exist but it might be straightforward to write a function yoursel…
Comment: R and GEO
by
ATpoint
48k
That is a microarray, you cannot load this into the IGV. IGV tracks assume some kind of count data.
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