User: gewa

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gewa0
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Posts by gewa

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Answer: A: trouble with tabix on generic file
... Resolved be restarting pipeline, I guess my file was corrupted. Sorry. ...
written 4 months ago by gewa0
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trouble with tabix on generic file
... Hi all, I'm trying to use tabix to index a custom, tab seperated file I have for fast access. The file is formatted such that the first 3 columns (tab seperated) represent a chromosome, start point, and end point respectively. It then has 4 more columns, each holding a number. The file is sorted and ...
tabix samtools written 4 months ago by gewa0
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Comment: C: Quickly retrieve reference genome sequence within python
... When I've tried using pyfaidx in the past, it's used nearly all my memory to load in the fasta. is this unexpected? ...
written 4 months ago by gewa0
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Quickly retrieve reference genome sequence within python
... Hi all, For a project I'm working on, I need to be able to quickly retrieve the sequence at a given 2kb window of the reference genome hg38 within python. The windows I need might not be consecutive (i.e. one thread might need to get the sequence for chr1:2500-4500 and another might need chrX:0-2000 ...
python sequence written 4 months ago by gewa0
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Comment: C: Fastest way to process fasta file?
... Thanks. I will try and come up with a chunking strategy compatible with my use case ...
written 5 months ago by gewa0
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Fastest way to process fasta file?
... Hi, I have a model that takes in a one-hot encoded sequence for a location on the human genome. However, I'm having trouble to find a way to not be limited by either time or space constraints when reading in the FASTA file with the sequences for the model. The file covers the whole human genome, so ...
fasta sequence written 5 months ago by gewa0 • updated 5 months ago by sacha1.6k
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Comment: C: Choosing a ChIP-seq control for Encode pipeline?
... Thanks for your response! I have actually already obtained the actual target run, from outside encode (in the link in my original post). It is a ChIP-seq on human H1, with SOX2 as the target (TF). I'm actually trying to find a control to use with it, and was wondering if I could get it from encod ...
written 6 months ago by gewa0
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Choosing a ChIP-seq control for Encode pipeline?
... Hi, I have a fastq file from a TF targeted ChIP-seq run, obtained from GEO here: https://www.ncbi.nlm.nih.gov/sra?term=SRX011616 I need to process this data and do peak-calling for some downstream stuff, and as I am using it in tandem with other data that the Encode project has already processed, ...
encode chip-seq written 6 months ago by gewa0 • updated 6 months ago by Alex Reynolds27k
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Comment: C: deeptools bamcompare/bamcoverage merging bins?
... I will try this and update with results, thanks! Also, is there any way you could please explain the calculation for the scale factor? I'm having trouble understanding where the 8 comes from, and why to use IDXstats. Thanks so much again! ...
written 7 months ago by gewa0
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deeptools bamcompare/bamcoverage merging bins?
... Hi all, I am currently using deepTools to process some chip-seq data and need a sanity check as to how to interpret/deal with the output, as I am not sure after reading the docs. I have some alignment files from multiple replicates of a ChIP-seq experiment targeting a histone mark. What I need to do ...
deeptools chip-seq written 7 months ago by gewa0 • updated 7 months ago by ATpoint13k

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Scholar 4 months ago, created an answer that has been accepted. For A: trouble with tabix on generic file

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