User: gewa

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gewa0
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Posts by gewa

<prev • 11 results • page 1 of 2 • next >
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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 24 days 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 24 days ago by gewa0 • updated 23 days ago by sacha1.5k
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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 4 weeks 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 4 weeks ago by gewa0 • updated 4 weeks ago by Alex Reynolds25k
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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 9 weeks 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 9 weeks ago by gewa0 • updated 9 weeks ago by ATpoint7.5k
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ChIP-seq normalization for input with RPKM
... Hi all, I'm currently trying to work off part of a paper (found [here][1]) involving processing some ChIP-seq data for histone modifications (ie H3K4me1). At one point (under "Histone Modication Inputs, Normalization, Preprocessing") the authors say: > The ChIP-seq reads of these histone mod ...
chip-seq written 10 weeks ago by gewa0 • updated 10 weeks ago by ATpoint7.5k
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Comment: C: Persistent parse and truncation errors sorting BAM files with samtools
... I have the same md5sum for my file -- I am assuming then that this issue is with my samtools version and will try 1.5. Thanks so much for the help! ...
written 11 weeks ago by gewa0
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Comment: C: Persistent parse and truncation errors sorting BAM files with samtools
... Hi, Yes, it is already coordinate sorted but I am unsure about all of the reference sequences used and wanted to ensure I could re-sort it if necessary. The file I am using specifically is: https://www.encodeproject.org/files/ENCFF592KJQ/@@download/ENCFF592KJQ.bam The experiment where the file is c ...
written 11 weeks ago by gewa0
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Comment: C: Persistent parse and truncation errors sorting BAM files with samtools
... Hey, I updated the original post with this information + the (improved) results of more troubleshooting (which was really just using the most recent version of samtools, 1.7, available). Let me know if I can add anything else that would be helpful ...
written 11 weeks ago by gewa0

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