User: Sam

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Sam70
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70
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United States
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3 years, 3 months ago
Joined:
3 years, 6 months ago
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Posts by Sam

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Binning BED file and counting antisense / sense reads
... This is great to hear! I'll sort this out today and let you know how it goes so I can accept your answer or ask additional questions. ...
written 3.4 years ago by Sam70
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Binning BED file and counting antisense / sense reads
... I am attempting to bin my BED file that contains gene intervals -2k/2k from the TSS. I would like to produce bins that are 1bp each. After binning I would like to count anti-sense and sense reads independently. The output data i'm looking for is: GeneID -2000 -1999 -1998 -1997 ...... 0 ...... 199 ...
gro-seq binning counting reads written 3.4 years ago by Sam70 • updated 3.4 years ago by Amitm1.6k
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How to obtain sense and antisense read counts from Gro-Seq data
... I am looking to obtain read-counts for sense and antisense strands from a GRO-Seq bedgraph file -2000/+2000 from the TSS for a set of genes in 1bp windows. Currently I am using HOMER with the -strand +/- -hist 1 -ghist option, is this appropriate?  Would htseq-count or bedtools coverage be better f ...
groseq read counts written 3.4 years ago by Sam70
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Comment: C: Looking for ways to download ChIP-seq datasets programmatically in a pipeline
... This is not related to the main question, since my experience is limited and wouldn't be very useful. But I am interested in testing these pipelines of yours if they are publicly available! ...
written 3.4 years ago by Sam70
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Comment: C: Same data, very different heatmaps
... I'm having trouble getting the heatmaps .cdt files to be sorted by Pol II density. The script that was left over by a former 'actual' bioinformatic person does not work because it relies on a very specific MySQL database that is based on RefSeq TSS annotation (and I am attempting to redo this using ...
written 3.4 years ago by Sam70
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Convergent Transcription Heatmap
... Hey everyone, so i'm here because i'm completely at a loss.  I recently read this paper (http://www.cell.com/cell/pdf/S0092-8674(15)00263-9.pdf) and was asked by my PI to reconstruct Figure 3. A using our ChIP-Seq and GRO-Seq data. Now while I'm primarily the only one in our lab that does any bioin ...
chip-seq net-seq heatmaps written 3.4 years ago by Sam70
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Comment: C: Same data, very different heatmaps
... Sorry yes you're right. Bedgraph files were indeed passed to the original command. That's my fault. The peakfile is actually a TSS file of RefSeq TSS. I've updated the example. I will attempt to run the command with a wig file instead of a bedgraph and see if there's a difference. ...
written 3.4 years ago by Sam70
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Comment: C: Same data, very different heatmaps
... You could be on to something. The bedfile given to homer is indeed the peak calls from MACS2 and is not the regions around the TSS. However, according to the ex lab member, what the heatmap is showing is each line represents a gene (~30k genes) and approximately 16.5k genes have Pol II in a -5k/5k w ...
written 3.4 years ago by Sam70
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Comment: C: Same data, very different heatmaps
... Would the results vary that much between peak files and bigwigs? I figured that might have something to do with it, but the difference is just so big. Scaling could definitely be a problem, JavaTreeViewer messes with scaling a lot. I've tried to make sure most default settings are tuned so that th ...
written 3.4 years ago by Sam70
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Comment: C: Overlapping regions in a BedGraph file
... Not surprisingly I got stuck quite quickly. Here's the edited script: (if you can call it that) import pyBigWig lastLine = None bw = pyBigWig.open("Gro-Seq.bdg", "w") bw.addHeader([("chr1", 249250621), ("chr2", 243199373), ("chr3", 198022430), ("chr4", 191154276), ("chr5", 180915260), ("chr6", 171 ...
written 3.4 years ago by Sam70

Latest awards to Sam

Scholar 3.4 years ago, created an answer that has been accepted. For A: Extracting promoter regions alignment
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Extracting promoter regions alignment
Student 3.4 years ago, asked a question with at least 3 up-votes. For Same data, very different heatmaps

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