User: a.rex

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a.rex110
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Posts by a.rex

<prev • 66 results • page 1 of 7 • next >
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Comment: C: How to compare bigwig tracks of two ATAC libraries.
... Ah....I get this error: bamCoverage: error: unrecognized arguments: CPM any clues? ...
written 5 days ago by a.rex110
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Comment: C: How to compare bigwig tracks of two ATAC libraries.
... Presumably as it’s rpm you can then directly compare the two tracks? Also is the bam the one directly following mapping? ...
written 5 days ago by a.rex110
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How to compare bigwig tracks of two ATAC libraries.
... I have two different ATAC-seq libraries that I wish to compare on a genome browser. I have used Macs to generate bedgraph files for each individual library using the command: macs2 callpeak -t macs2 callpeak -t bamfile --outdir /path/to/ -f BAMPE --keep-dup all --pvalue 1e-2 --call-summits --bdg ...
atac-seq written 5 days ago by a.rex110 • updated 5 days ago by ATpoint5.4k
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Comment: C: How can I look at find 'open chromatin' from ATAC-seq data using MACS2
... Hi ATpoint - I specifically want to identify enhancers (I also have H3K4me1 data for my model system). Problem is, I don't know whether to filter for short reads (i.e. <100bp). I see that some papers do this, others do not. ...
written 9 days ago by a.rex110
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Comment: C: How can I map reads only of a certain length?
... I presume if I change to '....> 140;' this will give me reads greater than 140? ...
written 10 days ago by a.rex110
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Comment: C: How can I map reads only of a certain length?
... Thank you ATpoint - I agree, I have also found NucleoATAC to be a bit difficult to comprehend. I have used your code, and after having plotted the NFRs, it does seem very similar but narrower than the full bam file. I suppose you could compare reads <100bp with that of mononucleosome reads (147-2 ...
written 10 days ago by a.rex110
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Comment: C: How can I map reads only of a certain length?
... Apologies, I mean fragment length. ...
written 11 days ago by a.rex110
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How can I map reads only of a certain length?
... I have recently done an ATAC-seq experiment - I wish to selectively map reads of <100bp from a fragment distribution of fragments from 20bp to 450bp following illumina next-seq PE sequencing. This way I can look at reads that most likely originate from nucleosome-free regions... How can I achi ...
atac-seq bwa sequencing written 11 days ago by a.rex110 • updated 11 days ago by Pierre Lindenbaum109k
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How can I look at find 'open chromatin' from ATAC-seq data using MACS2
... I am new to analysing ATAC-seq data. As mentioned on https://www.biostars.org/p/209592/, there seem to be two ways to use MACS to analyse ATAC-seq data. 1. Utilising the --shift -100 --extsize 200 command This, I believe, is to find where the cutting sites are. 2. Utilising the --shift 37 --e ...
macs2 atac-seq written 13 days ago by a.rex110 • updated 10 days ago by ATpoint5.4k
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How to demultiplex Unindexed.fastq.gz files?
... I have downloaded the Unindexed.fastq.gz files from my Next-seq run using the python downloader. How can I demultiplex these? Am I right in thinking that bcl2fastq requires bcl files? I do not understand why I cannot simply use the unindexed files that basespace generates? If this is not possibl ...
illumina bcl2fastq written 15 days ago by a.rex110 • updated 13 days ago by genomax51k

Latest awards to a.rex

Popular Question 5 weeks ago, created a question with more than 1,000 views. For createRepeatLandscape in RepeatMasker
Popular Question 6 months ago, created a question with more than 1,000 views. For Issues installing bcl2fastq?
Supporter 16 months ago, voted at least 25 times.
Student 18 months ago, asked a question with at least 3 up-votes. For mapping reads to repetitive elements in genome?

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