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:
8 hours ago
Joined:
4 weeks ago
Email:
a***********@gmail.com

Posts by akshay_ware

<prev • 11 results • page 1 of 2 • next >
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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 7 days ago by akshay_ware10 • updated 7 days ago by h.mon27k
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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 10 days 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 11 days ago by akshay_ware10 • updated 10 days ago by h.mon27k
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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 13 days 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 18 days ago by akshay_ware10 • updated 18 days ago by cschu1811.8k
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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 21 days ago by akshay_ware10 • updated 21 days ago by Kevin Blighe50k
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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 23 days ago by akshay_ware10 • updated 23 days ago by Devon Ryan92k
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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 26 days ago by akshay_ware10 • updated 26 days ago by ATpoint24k
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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 28 days ago by akshay_ware10
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Comment: C: Blastp not matching to reference more than 1000 entries.
... Yes, we are using very short query the command for creation of the database is : > makeblastdb -in ref.fasta -parse_seqids -titile "test" -dbtype prot and blastp command is: > blastp -query query.fasta -db ref.fasta -word_size 2 The query length is five amino acids ...
written 28 days ago by akshay_ware10

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