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Recent Replies
Answer: how to run and use the ENCODE ATAC-seq pipline
by
Jeremy Leipzig
20k
you might want to check out https://truwl.com/ - they have the official ENCODE ATAC-Seq pipeline as a runnable workflow
Comment: Can too high of a ChIPQC RiP% be indicative of insufficient stringency in peak c
by
ATpoint
48k
TFs can well have FRiPs in the 20% or 30% range, it is all on the antibody, expression level of the protein and quality of the chromatin. …
Comment: htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'
by
lieven.sterck
11k
I see, should be OK then I assume.
I remember that we needed to use the version that was installed in the python libs of a specific python…
Comment: htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'
by
Sara
•
0
I am using Python 3.7 (htseq-count specifies Python >=3.6)
Comment: Split fasta based on symbol and numeric position in header
by
Nick Scales
•
0
If possible in one step that would be great but I have already worked out how to do the second part of that with bedtools, for this I just …
Comment: Split fasta based on symbol and numeric position in header
by
Nick Scales
•
0
Okay this is super helpful thank you. My only need for the database is for it to have a fasta entry for each CAZyme so I can blast metageno…
Comment: htseq-count Error '_StepVector_Iterator_obj' object has no attribute 'next'
by
lieven.sterck
11k
are you using the correct python version?
Comment: Split fasta based on symbol and numeric position in header
by
GenoMax
100k
Just to clarify you want it to keep track of the aa number and then create a new record for each ID separated by `+` by taking into account…
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…
Comment: 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…
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