User: Payal

gravatar for Payal
Payal30
Reputation:
30
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New User
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5 hours ago
Joined:
1 year, 3 months ago
Email:
p********@gmail.com

Posts by Payal

<prev • 12 results • page 1 of 2 • next >
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Comment: C: 3 prime tag counting RNA Seq
... Yes its consistent among all samples..I aligned the fastq files to reference genome via Hisat2. I used Picard RNASeq Metrics to plot this graph. I just got to know this is FAC sorted data and it seems FAC sorted samples show this kind of 3prime bias..so i think i have to figure out how to do 3 prim ...
written 16 days ago by Payal30
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Comment: C: 3 prime tag counting RNA Seq
... This is how the graph looks,https://ibb.co/c7ou2H.. Is this normal? ...
written 17 days ago by Payal30
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3 prime tag counting RNA Seq
... Hi, I am currently working on an RNA Seq dataset, which has some 3 ' bias (I found that out by Picard RNASeq Metrics). So I was suggested to perfotm 3 prime tag counting. I came across this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3954844/ Can someone please explain to me how they are ...
rna-seq written 21 days ago by Payal30
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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 3 months 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 3 months ago by Payal30
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Comment: C: RNA SEQ ERCC
... Thanks... let me try those two options !!! ...
written 3 months 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 3 months 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 3 months 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 8 months ago by Payal30
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Answer: A: HISAT2 or Tophat2
... Thank you for all your suggestions. ...
written 15 months ago by Payal30

Latest awards to Payal

Supporter 10 weeks ago, voted at least 25 times.
Popular Question 8 months ago, created a question with more than 1,000 views. For HISAT2 or Tophat2
Teacher 8 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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