User: kdc15
kdc15 • 30
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Posts by kdc15
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... Hi,
No you are correct, MotifbreakR will be needed to predict TF binding from the SNP. I wanted to first identfiy what motifs were present in this sequence, but wanted to provide context as to why I was searching such a small sequence.
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written 6 days ago by
kdc15 • 30
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... I am trying to identify whether a SNP will affect TF binding. Here is the DNA sequence that I have obtained:
>hg19_dna range=chr21:39819567-39819957 5'pad=0 3'pad=0 strand=+ repeatMasking=none
TAGACTTAGTCATGCTAATTAAGACAAAAATTAGACCTTATTAAAAAATT
TTTGCAAAACAGATACTCCCTTCCCATGGTGGCACTGGC ...
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Comment:
C: Can't locate Bowtie2 index files
... Thank you, I have managed to do this now. Looks like I was using Bowtie1 instead of Bowtie2 ...
written 7 weeks ago by
kdc15 • 30
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Comment:
C: Can't locate Bowtie2 index files
... Thank you, this helped!! ...
written 7 weeks ago by
kdc15 • 30
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Comment:
C: Can't locate Bowtie2 index files
... I got the files from this page under pre-built indexes: http://bowtie-bio.sourceforge.net/tutorial.shtml#preb ...
written 7 weeks ago by
kdc15 • 30
5
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... Hi,
I am trying to align my sequences to a reference genome but Bowtie2 is having trouble locating the index files that I downloaded from Illumina. I am working on a server and have read instructions about moving the files to the bowtie2 index subdirectory, however, this does not exist. It also sa ...
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... Would someone be able to explain what are the differences in these two algorithms for motif finding? I am having trouble fully understanding what are the main differences, and which is a better approach to use.
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written 10 weeks ago by
kdc15 • 30
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... for my -incl option I have selected the mappable regions (with a CRG score of 1) of the genome. Is it better to replace this with my enhancer file? ...
written 3 months ago by
kdc15 • 30
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... Hi, I am trying to use the bedtools shuffle command to shuffle transcription factor binding locations. However, I was wondering if the "genome" option could be interchangeable with my own customised file of enhancers? Is it possible to have a file like this in the same format?
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... Hi,
I would like to filter a .bed file by numbers in the last column:
chr1 0 14400 18
chr1 14400 19000 6
chr1 19000 567400 18
chr1 567400 567800 10
chr1 567800 713200 18
chr1 713200 713800 2
chr1 713800 714600 1
chr1 714600 715400 2
chr1 715400 724000 6
Ho ...
written 4 months ago by
kdc15 • 30
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