User: anshupa.vssut

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Posts by anshupa.vssut

<prev • 17 results • page 1 of 2 • next >
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Tools for polyA site identification in DNA sequences
... I am currently looking for tools which can help me to identify polyA sites in DNA sequence. Any suggestions for the same? I checked in omicstools.com regarding the same but most of the tool mentioned there were restricted to RNA sequence. ...
polya written 8 months ago by anshupa.vssut20 • updated 8 months ago by Andy20
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Comment: C: Identifying long stretches of Ns
... I am looking for regions were it is obvious to find gaps (N's) in hg19, I am not looking into hard masked repeat regions. ...
written 12 months ago by anshupa.vssut20
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Identifying long stretches of Ns
... Is there a R package to identify long stretches of gaps (Ns) in human genome (hg19)? ...
genome R written 12 months ago by anshupa.vssut20 • updated 12 months ago by ATpoint9.1k
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Comment: C: Using SeqAn and other external libraries in C++
... Thanks a lot, the issue got resolved after adding -std=c++14 to g++ command. Thanks again. ...
written 13 months ago by anshupa.vssut20
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Using SeqAn and other external libraries in C++
... Hello All, I am new to C++ and also to using external libraries in C++. I am currently trying to use SeqAn for read mapping. I have created a Test.cpp with the following code: #include #include #include using namespace seqan; int main() { std::cout << CharStr ...
testing seqan tutorial seqan read mapping written 13 months ago by anshupa.vssut20
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Comment: C: Comparing position weight matrices
... I have already performed this analysis. I am currently looking for methods to handle short sequences of length upto 30 bp which are enriched for SNVs but are not identified by FIMO. For that, I represent these short sequences as position weight matrix(PWM) and intend to compare this with existing PW ...
written 16 months ago by anshupa.vssut20
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Comparing position weight matrices
... Hello All, I have my sequences represented as position weight matrix and wish to check for transcription factors occurring in those sequences. Can anyone suggest a tool that compares position weight matrices? ...
position weight matrix transcription factors written 16 months ago by anshupa.vssut20 • updated 16 months ago by WouterDeCoster33k
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Interpret fimo results in negative strand
... I have a simple question regarding interpreting fimo results in the negative strand. I got the following result in negative strand for transcription factor STAT3. HNF4A 295 315 STAT3_HUMAN.H10MO.A 12.7879 - 1.15e-05 0.118 ATGCAAGCTTGGCCAAGCCC Here Start position ...
fimo transcription factors motifs written 16 months ago by anshupa.vssut20 • updated 16 months ago by genomax58k
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Extract motif ids of all transcription factors in human
... Hello all, I wish to extract the motif ids of all transcription factors occurring in humans from JASPAR 2016. Is anyone aware of how to achieve this? ...
humans transcription factor jaspar written 17 months ago by anshupa.vssut20 • updated 12 months ago by asntech30
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Data retrieval icgc
... Is there a command line tool or r package to efficiently retrieve datasets from ICGC? ...
icgc r-package written 21 months ago by anshupa.vssut20

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