User: anshupa.vssut

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Posts by anshupa.vssut

<prev • 16 results • page 1 of 2 • next >
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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 5 weeks 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 5 weeks ago by anshupa.vssut20 • updated 5 weeks ago by ATPoint2.6k
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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 8 weeks 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 8 weeks 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 5 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 5 months ago by anshupa.vssut20 • updated 5 months ago by WouterDeCoster24k
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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 5 months ago by anshupa.vssut20 • updated 5 months ago by genomax39k
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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 5 months ago by anshupa.vssut20 • updated 27 days 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 10 months ago by anshupa.vssut20
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Converting Vcf File To Maf
... I have a vcf file generated by in-house variant calling pipeline, containing both coding and non-coding SNVs can anyone suggest a tool or R-package for converting the vcf file to maf format? I needed to file in MAF format to visualize the mutation landscape using genvisr ...
vcf maf non-coding written 11 months ago by anshupa.vssut20 • updated 11 months ago by mbyvcm330

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