User: varsha619

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varsha61970
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Posts by varsha619

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Comment: C: fasta to bed format with more information that just chr locations
... Thank you! I liked the 2nd method the best and seemed to be the easiest to use - cut -f2,3 -d";" test.txt| cut -d= -f2,3 | awk -v OFS="\t" -F':|=|;|\\..|{' '{print "chr"$1,$2,$3,$5}' ...
written 19 days ago by varsha61970
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Comment: C: fasta to bed format with more information that just chr locations
... @Daniel, would you mind explaining how the columns $5 and $10 are defined, when I run the script it does not output the right values. And yes I would like the output values to be tab separated. Thanks! ...
written 20 days ago by varsha61970
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fasta to bed format with more information that just chr locations
... Hello, I have a fasta file with lines of format - >FBti0019256 type=transposable_element; loc=2L:22300300..22304444; name=invader2{}555; dbxref=FlyBase_Annotation_IDs:TE19256,FlyBase:FBti0019256; MD5=d9259a0e33aad699215e64916bd47a5b; length=4145; release=r6.19; species=Dmel; I would ...
fasta to bed written 20 days ago by varsha61970 • updated 20 days ago by Daniel3.6k
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Comment: C: using MACS2 with hg38
... Hi Igor, thank you for your reply. Do you think it's ok for the files to be aligned to hg38 and MACS2 run with the -g/--gsize parameter? ...
written 9 weeks ago by varsha61970
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using MACS2 with hg38
... Hi! I am wondering if there has been any updates regarding using MACS2 with hg38. I have my files aligned to hg38 and used genome option in MACS2 as default for 'hs' which I am not sure is still hg18 or if it has been updated to hg38. Please let me know, thank you! ...
macs2 hg38 written 9 weeks ago by varsha61970 • updated 9 weeks ago by igor6.0k
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Comment: C: bp overlap between multiple beds
... Thank you for your help Alex! I got the bedops and awk commands to work, as well as ended up using the 'intervene pairwise' module which gave me significance of overlap between bed files. ...
written 3 months ago by varsha61970
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Comment: C: bp overlap between multiple beds
... Thanks for the explanation Alex, I understand the method now. I have 3 files A.bed B.bed C.bed and when I do the last step - bedmap --count --bases-uniq --delim '\t' partition.bed union.bed The resulting file had values of 4 and 5 in column 1, which from your explanation is the number of fil ...
written 3 months ago by varsha61970
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Comment: C: bp overlap between multiple beds
... Hi Alex, I am a little confused with the output of bedmap. Is the 1st column number of overlaps and 2nd column bp overlap? 2 153 1 70 2 88 Is there a way to also see which files have these overlaps? Thank you!! ...
written 3 months ago by varsha61970
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bp overlap between multiple beds
... Hello, I was wondering what would be the best tool to identify and plot a venn of number of bp overlap between more than 3 bed files (similar to bedtools intersect -wo for 2 files). I have read all the related threads on multiInter and bedops. I also tried Homer mergePeaks --venn option and I ...
bedtools venn multiinter written 3 months ago by varsha61970 • updated 3 months ago by Alex Reynolds23k
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Comment: C: Finding An Genomic Intervals Shared For A Given Individual As Called By Two Or M
... Hello, this works great to compare multiple bed files. Though I was wondering if there is an option in multiIntersectBed to output the number of bp overlap between multiple bed files (similar to bedtools intersect -wao option). Please let me know, thank you! ...
written 3 months ago by varsha61970

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Which ChIP-seq IgG to use?
Popular Question 11 months ago, created a question with more than 1,000 views. For How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files

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