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Recent Replies
Comment: Split fasta based on symbol and numeric position in header
by
heskett
•
0
You need to explain what functions you want the database to have. if you use GTF format than this will be readable by alignment programs su…
Answer: Looking for a Whole Genome Sequencing GrCH38 Control group of roughly 250 sample
by
heskett
•
0
As mentioned, raw sequencing data of humans is privacy protected by law because it is identifiable. You need to either use a high-level sum…
Comment: Split fasta based on symbol and numeric position in header
by
Nick Scales
•
0
Thanks for the response - I tried this and it looks like it gives me the same output as the biopython script, which is the sequence and the…
Answer: Rare cell population in single cell ATAC-Seq
by
heskett
•
0
Yes this is possible. There's now likely hundreds of research papers that use single cell ATAC seq to do exactly this task, if you read may…
Answer: How to get GSE data into IGV
by
heskett
•
0
I'm not super familiar with GSE, but you should realize that IGV will readily accept BAMs, BEDs, and VCFs. If you want to view ChiP-seq pea…
Comment: Split fasta based on symbol and numeric position in header
by
Nick Scales
•
0
Thanks for getting back to me - I could see why that would be advantageous. Is there a tool that I could use if I went back a step and put …
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…
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