User: kimkes25

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kimkes250
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Posts by kimkes25

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Databases for genome accessibility
... you are totally right. I just upvoted answers! Thank for the comment! I fixed my post. also ataq-seq will be great! My goal is to find experiment results for a list of cells that has accessability scores for the genome. after I have that, I will check the correlation between open areas to crispers ...
written 1 day ago by kimkes250
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Databases for genome accessibility
... Hello. I am looking for dnase-seq resuls for certain cell types in narrow peak format. I tried to find results on ENCODE and UCSC with no success. Where else should I look for it? Do you know any other databaese online? Thanks ...
dnase encode accessibility ucs written 1 day ago by kimkes250
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help with finding dnase resuls for certain cell types
... Hello. I would like to find dnase-seq resuls for certain cell types in [narrow peak format.][1] I found in [this][2] link the results for **hek293** cell type > wgEncodeOpenChromDnaseHek293tPk.narrowPeak.gz 03-Feb-2012 12:28 1.9M I would like to find this kind of r ...
dnase narrow peak written 4 days ago by kimkes250
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Learning how to use Samtools
... Hello. I am working with narrowpeak and bed files. I want to use samtools in order to index( tabix) the files. I want to use it also in order to conduct queries on my files. The documentation in the website is not so informative and doesn't refer my type of files directly. How can I learn how t ...
samtools written 10 days ago by kimkes250 • updated 9 days ago by ATpoint40k
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retrieving rows from a bed file
... Hello . my goal is to have this kind of bed file: and be able to enter a **chrom** number and a range between **chromeStart** and **chromeEnd**, and to recieve all rows that match it. what is the best way to do it? Thanks ...
bed written 11 days ago by kimkes250 • updated 11 days ago by Alex Reynolds31k
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bed file indexing problem
... Hello. I have a bed file that looks like this: I would like to be able to retrieve data from it using samtools with tabix. the actions I do: - bgzip sample.bed - **-tabix -s 1 -b 2 -e 3 sample.bed.gz** - tabix sample.bed.gz chr1:19922842-19924305 but I have a problom after trying the ...
dnase1 bed tabix samtools bed file written 11 days ago by kimkes250
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Comment: C: How to download BED file with all the fields?
... I fixed it now .can u take another look please? ...
written 15 days ago by kimkes250
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Comment: A: How to download BED fiile with all the fields?
... I meant when I download the file with output format "all fields from selected table" (with save as) I get this weird file: ![downloaded outpu][5] ( I got it by clicking save as from the tab that opened that is what I want) ![output in new tb][4] [1]: https://ibb.co/ThrsKsR [2]: https://ibb.c ...
written 15 days ago by kimkes250
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How to download BED file with all the fields?
... Hello, **my goal** : to download a certain BED file from ucsc website that contains all these fields: bin chrom chromStart chromEnd name score strand signalValue pValue qValue peak I will describe my actions and my problem: - I go into the [table browser][1](tools>Table Browser) and choose ...
bed ucsc written 15 days ago by kimkes250
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Comment: C: how to to download a BED file from ucsc to directory using linux
... before the gzip issue- when I try to save it as ".bed" it saves it as "bed.txt" and I want it as "bed" ...
written 16 days ago by kimkes250

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