User: prathyushakonda

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New User
Location:
Halifax, Canada
Website:
https://github.com/Pra...
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1 year, 1 month ago
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3 years ago
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Posts by prathyushakonda

<prev • 10 results • page 1 of 1 • next >
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MACS2 MODEL VS NO MODEL FOR CHIRP SEQ
... Hi guys, This is a very related problem with MACS2. I am doing peak calling of my 'chirp' seq data, using SAM files, treatment and input contain tag length of 126bp. I noticed the classic 'Since the d (20) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown s ...
chirp-seq macs2 chip-seq peakcalling written 15 months ago by prathyushakonda20
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What is the recommended sequencing depth for ChIRP-seq?
... Hi, we are planning to do chirp-seq for a lncRNA of interest. The company uses HiSeq2000 for this. We are wondering about what sequencing depth is ideal for this. Would 100 mil. reads be sufficient enough to get good coverage? I would greatly appreciate your valuable insights. ...
sequencing chip-seq rna-seq lncrna written 23 months ago by prathyushakonda20
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Comment: C: Converting a mutation data file into vcf?
... Sorry about that. This is how it looks. Gene_Name Sample_Name CDS_Mutation AA_Mutation 39340 05-165O c.71C>T p.T24I A1BG 06-134H1 c.330G>A p.L110L A1BG TCGA-CH-5752-01 c.480G>A p.E160E A1BG TCGA-EJ-5499-01 c.733C>T p.R245C A1CF DU-145 c.688G>T p.V230L ...
written 2.0 years ago by prathyushakonda20 • updated 2.0 years ago by WouterDeCoster39k
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Converting a mutation data file into vcf?
... Hello, I have a dataset of mutations which consists of information about gene, CDS mutation, sample and AA mutation. I was wondering if there are tools to annotate this kind of data? Is it possible to convert this to vcf at all? or is there an easier way to generate consensus sequences based on this ...
exome bioinformatics next-gen sequencing written 2.0 years ago by prathyushakonda20 • updated 22 months ago by Biostar ♦♦ 20
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Comment: C: RESOLVED: libgtextutils make error : FASTX toolkit
... Hello Pierre, This is odd but my file doesn't have this. i = close(fd); if ( fd == -1 ) err(1,"close(in pipe_close) failed"); p = waitpid(pid, &status, 0); if (p==-1) err(1,"waitpid(in pipe_close) failed"); if (!WIFEXITED(status)) errx(1," ...
written 2.2 years ago by prathyushakonda20 • updated 2.2 years ago by RamRS22k
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RESOLVED: libgtextutils make error : FASTX toolkit
... Hi, I am trying to install FASTX toolkit by following the instructions from their website. http://hannonlab.cshl.edu/fastx_toolkit/install_ubuntu.txt While installing libgtextutils, make command gives following error: make all-recursive make[1]: Entering directory '/media/wkstn/Data/Cou ...
ngs fastx 16s rrna genomics rna-seq written 2.2 years ago by prathyushakonda20 • updated 2.2 years ago by Charles Plessy2.7k
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Anyone familiar with proggene risk analysis?
... Hi, I recently used proggene for survival analysis, which majorly uses NCBI-GEO data. Is anyone familiar about the usage or implementation of the risk summary that the web tool provides at the end of analysis? I understand that proggene itself works by using R based analysis, but I am trying to use ...
ncbi survival curve cancer written 2.4 years ago by prathyushakonda20 • updated 2.4 years ago by bruce.moran620
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Comment: C: Exome Seq Data analysis - chromosome start and end positions
... That makes sense. I think it's snp array. I was confused because the website and the file name said exome seq data. Thank you, Vakul Monhanty! ...
written 2.8 years ago by prathyushakonda20
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Exome Seq Data analysis - chromosome start and end positions
... Hello, I am an immunology student learning bioinformatics. I was searching to find the right answer for the problem I have but haven't found any concrete explanation. I have an exome seq data file downloaded from a public database. The excel file contains details regarding ProbeID, gene name, gene ...
next-gen exome-seq rna-seq snp written 2.8 years ago by prathyushakonda20
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Comment: C: What'S The Best Way To View And Explore A Large Gene Ontology Dag?
... I had tried Reivogo recently, I was not able to customize the node or edge variables after taking into cytoscape. Have you guys experienced anything like this? ...
written 2.9 years ago by prathyushakonda20

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Popular Question 13 months ago, created a question with more than 1,000 views. For RESOLVED: libgtextutils make error : FASTX toolkit

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