User: akshay_ware

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akshay_ware10
Reputation:
10
Status:
New User
Location:
Manipal School of Life Science
Twitter:
@akshay_ware12
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Google Scholar Page
Last seen:
22 hours ago
Joined:
9 months, 2 weeks ago
Email:
a***********@gmail.com

Posts by akshay_ware

<prev • 12 results • page 1 of 2 • next >
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Comment: C: How to extract the list of genes from TCGA CNV data
... Sir, as you mentioned pre-computed GISTIC 2.0 data for "UCEC.Level_3_segmented_scna_minus_germline_cnv_hg19.seg.txt" this file. I am not understanding whether this is input or output of GISTIC 2.0. Is this file compiled version of tcga cnv data? can i use this file for gistic analysis? Thank you ...
written 6 months ago by akshay_ware10
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How to find adaptor sequences from SRA sample?
... Hi, I am doing small RNA sequencing data analysis from SRA database. I want to know which are the adapter sequences are present in that samples. how do I get that? Thank You ...
alignment next-gen rna-seq sequencing written 8 months ago by akshay_ware10 • updated 8 months ago by h.mon30k
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Comment: C: Error in installation of RandFold 2.0
... Hello, I am using Ubuntu 18.4 I am not using conda. I am trying to install Cap-MirSeq pipeline in that i am facing error. as posted earlier. when I tried RandFold 2.0 alone, it was installed properly but not with pipeline. Thanks ...
written 9 months ago by akshay_ware10
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Error in installation of RandFold 2.0
... I am trying to install RandFold 2.0, got following error: fold.o: In function `fill_arrays': fold.c:(.text+0x115c): undefined reference to `HairpinE' fold.c:(.text+0x12ca): undefined reference to `LoopEnergy' fold.o: In function `backtrack': fold.c:(.text+0x3d48): undefined refe ...
ubuntu linux rna-seq bioinformatics written 9 months ago by akshay_ware10 • updated 9 months ago by h.mon30k
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How can I get Adapter information for SRR File from SRA ?
... Hi, I am doing RNA-Seq analysis on sequencing data from SRA. I want to remove the adapters from the file. how can i get to know, what adapter sequences they used while sequencing? Or how can I trimmed this adapters? Thank you ...
assembly next-gen rna-seq alignment sequencing written 9 months ago by akshay_ware10
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Can I use TruSeq2-SE.fa blindly given in Trimmomatic?
... Hi, I am working on small RNA-Seq data analysis, I have query regarding trimmomatic tool which widely used for adapter trimming from reads. In the command below: trimmomatic SE -phred33 input.fastq Out_trimmomatic.fastq ILLUMINACLIP:/trimmomatic-0.38-1/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 ...
assembly next-gen rna-seq alignment sequencing written 9 months ago by akshay_ware10 • updated 9 months ago by cschu1812.3k
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How to build reference index for bowtie?
... I am aligning RNA-Seq data to human genome reference hg38. How can I build the index using hg38.fa Thanks in advance ...
assembly next-gen rna-seq alignment written 9 months ago by akshay_ware10 • updated 9 months ago by Kevin Blighe61k
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When to run fastq-dump --split-files -X 10000 ?
... I am doing RNA-Seq data analysis of SRA data. I am not understanding the purpose of command fastq-dump --split-files -X 10000 Why to split file? and if i don't know the data is paired end or single end. is there is need to use -X 10000 ? Thanks in advance ...
assembly next-gen alignment rna-seq sequencing written 9 months ago by akshay_ware10 • updated 9 months ago by Devon Ryan95k
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Can I combine RPM values of RNA datasets from tow different databases?
... I have RPM values of RNAs (eg.blood) from 2 different databases. Can I combine the blood sample RPM data from two different databases? ...
rna rna-seq genomics sequencing written 9 months ago by akshay_ware10 • updated 9 months ago by ATpoint36k
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Comment: C: Blastp not matching to reference more than 1000 entries.
... Hi, By adding the -evalue 10000 the query returned with the right match. Thank You! ...
written 9 months ago by akshay_ware10

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