User: ashjay

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ashjay20
Reputation:
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Status:
New User
Location:
Madison, WI
Last seen:
2 years, 5 months ago
Joined:
2 years, 9 months ago
Email:
a**************@gmail.com

Posts by ashjay

<prev • 9 results • page 1 of 1 • next >
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Answer: A: HOMER motif discovery gives inconsistent results on repeated runs
... So HOMER *de novo* motif discovery works by comparing peak sequences (binned by length) to background sequences (of matched length) and calculating enrichment. It randomly generates the background sequences with every run, so you would expect some variability over different runs. I worked around thi ...
written 2.7 years ago by ashjay20
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Comment: C: Bedtools and BEDOPS closest/closest-features issues
... Edit: The duplicate gene names are different isoforms. ...
written 2.7 years ago by ashjay20
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Comment: C: Bedtools and BEDOPS closest/closest-features issues
... Hey thanks - the file wasn't sorted because the motif bed file was in the MAC text format. I used HOMER's changeNewLine.pl utility to change to UNIX format, sorted and then used closest and it worked. Now I have each peak annotated twice for some reason but working on that:) ...
written 2.7 years ago by ashjay20
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(Closed) Bedtools and BEDOPS closest/closest-features issues
... I have a bed file with hg19 motif coordinates that I would like to annotate. I downloaded the hg19 refFlat bed file from UCSC and (after sorting both files with the sort function) tried to use the closest function in bedtools to annotate the closest gene. However, I my output only shows the followin ...
bedtools bedops written 2.7 years ago by ashjay20
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Comment: C: TopHat deletions and insertions
... 1) So if an alignment works best with a gap, we consider the gap to be a deletion and vice versa for an insertion? 2) Maybe I'm missing something but this is all I found about insertions and deletions on the TopHat man page: > insertions.bed and deletions.bed. UCSC BED tracks of insertions and ...
written 2.8 years ago by ashjay20
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Comment: C: TopHat deletions and insertions
... Sure - TopHat produces a deletions.bed and insertions.bed file. 1) How are these insertions and deletions identified? 2) When mapping reads to the genome, we allow for a certain number of mismatches and gaps - how do these relate to how tophat identifies deletions and insertions? ...
written 2.8 years ago by ashjay20
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TopHat deletions and insertions
... How are the TopHat deletions and insertions identified? How does this relate to the mismatch and other alignment options used? I'm a little confused and would appreciate an explanation. Thanks! ...
alignment rna-seq written 2.8 years ago by ashjay20 • updated 2.8 years ago by Fabio Marroni2.2k
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Comment: C: Small RNA seq dataset with NNN addition
... You can use [cutadapt][1] to trim out the Ns & low quality bases in addition to removing reads with all Ns. To remove flanking N bases: cutadapt --trim-n To remove reads with more than COUNT number of Ns: cutadapt --max-n COUNT [1]: http://cutadapt.readthedocs.io/en/stable/guid ...
written 2.8 years ago by ashjay20
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Comment: C: Small RNA seq dataset with NNN addition
... > N + 20 something nt miR sequence Do you know its a miR sequence? Have you tried filtering out the all N containing reads, trimming out the N's in the rest of the reads and then mapping them? If you did, what does the expression profile look like? What percent of reads are all Ns? Sounds lik ...
written 2.8 years ago by ashjay20

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