User: Payal

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Payal30
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5 days, 16 hours ago
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1 year ago
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Posts by Payal

<prev • 9 results • page 1 of 1 • next >
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Answer: A: RNA SEQ ERCC
... What I did to make it work: Previously I installed Tophat 2.1.1 and Bowtie 2.2.5 via Bioconda. I was getting the error because for some reason these versions of Tophat and Bowtie doesn't work together. So I installed Tophat from Source on my system. First I installed 2.1.1 - the plain topahat ru ...
written 17 days ago by Payal30
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Comment: C: RNA SEQ ERCC
... Yup I did look into this post while looking for answers... another problem I found was if the genome and gtf files don’t have same annotation then it can throw errors, so I downloaded both the gtf and genome fa file from Ensemble db!!! ...
written 4 weeks ago by Payal30
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Comment: C: RNA SEQ ERCC
... Thanks... let me try those two options !!! ...
written 4 weeks ago by Payal30
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Comment: C: RNA SEQ ERCC
... For now thats the only server I have..we are trying to increase our capabilities!! But for now thats all I have got to work with!! I am sorry but I don't have an answer to why they included ERCC spikeins because neither was I not involved in the study design or the wet lab part of the experiment. A ...
written 4 weeks ago by Payal30
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RNA SEQ ERCC
... Hi, I am trying to analyze a RNA seq dataset with ERCC spike ins. I am using Tophat because I am also supposed to look at fusion genes and so far I haven't found a proper pipeline for that!! (Yes I know STAR has STAR fusion but STAR just crashed (32GB). I don't think HISAT has fusion detection func ...
ercc tophat rna-seq bowtie written 4 weeks ago by Payal30
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Kraken Database Installation Problem
... Hi, I am trying to install and run Kraken for a metagenomics project. I have installed Kraken, however it requires a dependent database to be built as well. I am trying to build the database following their manual, where I am supposed to run: **kraken-build --standard --db dir/dbname** However I ...
metagenomics written 5 months ago by Payal30
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Answer: A: HISAT2 or Tophat2
... Thank you for all your suggestions. ...
written 12 months ago by Payal30
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HISAT2 or Tophat2
... Hi I am new to rna seq..I would like to know which one of Tophat2 and Hisat2 is the better aligner for rna-seq data? Or is there an even better option? ...
alignment rna-seq written 12 months ago by Payal30 • updated 12 months ago by Charles Warden4.9k
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Answer: A: How to download raw sequence data from GEO/SRA
... Addition:(Further Downstream RNA-Seq Analysis using GALAXY) In case anybody wants to get files from SRA directly into GALAXY for further analysis, please check out this other video too, https://www.biostars.org/p/117518/. It explains how to get data from SRA directly into GALAXY using Tools in GALA ...
written 12 months ago by Payal30

Latest awards to Payal

Popular Question 5 months ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How to download raw sequence data from GEO/SRA

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