User: jennxyzhang

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Posts by jennxyzhang

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ChIP-seq Differential Binding analysis for specified genomic regions of interest? (DiffBind/csaw?)
... I'm trying to figure out how to perform a ChIP-sew differential binding analysis on specific regions of interest (in my case a 1kb upstream region of specific transposons). I have ChIP-seq data for various cell lines and two histone markers of interest (H3K4me3, H3K27ac), but only one replicate of ...
csaw R diffbind differential binding chip-seq written 3 months ago by jennxyzhang0 • updated 3 months ago by ATpoint41k
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Comment: C: No space left on device error with deeptools bamCompare
... Is it possible to reallocate more space for the root directory? Can't find much to remove.. ...
written 4 months ago by jennxyzhang0
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No space left on device error with deeptools bamCompare
... Hello! I'm running a few scripts right now on a server and whenever I run bamCompare I get the 'no space left of device' error. $ df -H Filesystem Size Used Avail Use% Mounted on /dev/xvda1 16G 16G 0 100% / none 4.0K 0 4.0K 0% /sys/fs/cgroup u ...
software error deeptools picard terminal bash written 4 months ago by jennxyzhang0 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: deeptools computeMatrix reference-point, want to plot 1kb before TSS and 1kb aft
... I don't want to plot the gene bodies, just the regions before and after, with a little tick to mark the gene is located in the middle. I think there might just be no easy workaround with plotHeatmap so I might just need to plot it myself. :') Thanks ...
written 4 months ago by jennxyzhang0
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deeptools computeMatrix reference-point, want to plot 1kb before TSS and 1kb after TES then use plotHeatmap
... Hello! I am looking to use deeptools plotHeatmap to plot 1kb before and after a gene annotation. Unfortunately I don't think computeMatrix allows me to do this as I can only select one reference-point. What I tried instead was to run computeMatrix for the 1kb upstream of TSS, and separately run 1k ...
software error deeptools chip-seq written 4 months ago by jennxyzhang0 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: igvtools count | wigToBigWig, pipe not working for some reason although stdout a
... Thank you very very much for your suggestions! Unfortunately I'm still getting that same pop up "Unrecognized line 1 of stdin:" I'll stick with running these two commands separately. ...
written 4 months ago by jennxyzhang0
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igvtools count | wigToBigWig, pipe not working for some reason although stdout and stdin should work with both commands?
... Hi I am trying to pipe the output .wig format of igvtools count to wigToBigWig to convert to .bw format. Here is my code: igvtools count -w 10 -f median $file stdout hg19 | wigToBigWig stdin hg19.chrom.sizes ${name}.bw I have also tried: igvtools count -w 10 -f median $file stdout hg19 | ...
software error chip-seq written 4 months ago by jennxyzhang0 • updated 4 months ago by Pierre Lindenbaum131k
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Downloaded fastq from SRA, am I right in thinking it isn't interleaved paired-end reads?
... Downloaded fastq from SRA using fasterq-dump I used grep on a sequence identifier I pulled using head: **grep HWI-ST808:122:C1B50ACXX:2:1101:2426:2231 C1_p_K4me3.fastq** output: **@SRR1035416.1 HWI-ST808:122:C1B50ACXX:2:1101:2426:2231 length=51** **+SRR1035416.1 HWI-ST808:122:C1B50ACXX:2:1101:2 ...
sequencing written 5 months ago by jennxyzhang0 • updated 5 months ago by genomax92k

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