User: barrypraveen

gravatar for barrypraveen
Reputation:
0
Status:
New User
Last seen:
4 hours ago
Joined:
3 weeks, 6 days ago
Email:
b***********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by barrypraveen

<prev • 26 results • page 1 of 3 • next >
0
votes
1
answer
50
views
1
answer
Error: duplicate GFF ID 'ENST00000400518' encountered! [FAILED] Error: could not execute cuffcompare
... Hi folks, When I run cuffmerge I have used this command cufflinks Version - cufflinks_2_2_1 cuffmerge -p 16 -o ~/RNA_HOME/cuffmerge/merged -g ~/RNA_HOME/refs/hg19/genes/genes_chr22_ERCC92.gtf ~/RNA_HOME/de_novo/assembly_GTF_list.txt **Error: duplicate GFF ID 'ENST00000400518' encountered! ...
software error next-gen rna-seq written 5 hours ago by barrypraveen0 • updated 2 hours ago by i.sudbery990
0
votes
1
answer
41
views
1
answer
(Closed) Difference between single end and paired end library preparation in RNA Sequencing?
... Dear friends, I am from bioinformatics background. I started to learn about RNA Sequencing analysis. Before that I have some basic doubts please that clear off. Difference between single end and paired end of cDNA library preparation in RNA Sequencing? please explain. ...
ngs rna-seq sequencing written 3 days ago by barrypraveen0 • updated 3 days ago by Medhat6.1k
5
votes
1
answer
119
views
1
answer
How to differentiate SNPs Vs Sequencing error in RNA Seq?
... Dear all, I am learning RNA Sequencing. So i want to know some basic stuff. In RNA Seq data some sequencing error also possible but it has SNPs also how to do differentiate or any other way to figure out.. ...
next-gen rna-seq snp written 4 days ago by barrypraveen0 • updated 4 days ago by Dan Gaston6.5k
0
votes
1
answer
137
views
1
answers
Comment: C: I want to know about the actual function of Bowtie?
... Thank you very much. I uesd this command. In tophat it has two things tophat and tophat2. Is there any difference between tophat and tophat2. But i did tophat /opt/tophat_2_0_11/**tophat** -p 16 -r 60 --library-type fr-firststrand -o TopHat_OUPUT -G ~/ACTREC_RNA/Annotation/genes.gtf ~/ACTREC_RNA/bw ...
written 8 days ago by barrypraveen0
0
votes
0
answers
81
views
0
answers
Comment: C: how to use -u/--multi-read-correct and -b/--frag-bias-correct ?
... Thanks for your reply, No i didn't get any error but i want to know did i anything wrong. Actually i was confused -u default is FALSE but here i gave .gtf file it is correct? ...
written 9 days ago by barrypraveen0
1
vote
0
answers
81
views
0
answers
how to use -u/--multi-read-correct and -b/--frag-bias-correct in my command?
... In my cufflinks_2_0_2 i have to use -u parameter and -b parameter. how do i use? i have used this command /opt/cufflinks_2_0_2/cufflinks -p 8 -o condition **-u** **-b** --GTF ~/ACTREC/annotation/genes.gtf ~/ACTREC/Tophat/Tophat_P10_Rep1/accepted_hits.bam (for your understanding i have highlig ...
software error ngs rna-seq written 9 days ago by barrypraveen0
0
votes
1
answer
137
views
1
answers
Comment: C: I want to know about the actual function of Bowtie?
... Thank you for your reply. First point is i have to replicate the data that is why i am using tophat. I am confused at this step. In bowtie command, i didn't use any fastq file so that (My doubt is without fastq file how to do bowtie align). At which step bowtie do align. Next doubt is what is the fu ...
written 9 days ago by barrypraveen0
0
votes
1
answer
137
views
1
answers
Comment: C: I want to know about the actual function of Bowtie?
... 1. Thanks for your answer. bowtie-build creates indexing so that file stored in .bt format. I am using this command `(/opt/bowtie2_2_2_1/bowtie2-build ~/ACTREC_RNA/Ref/genome.fa ~/ACTREC_RNA/bwt/genome/genome)`. My doubt is without fastq file how to do bowtie align. before running tophat i import ...
written 10 days ago by barrypraveen0 • updated 10 days ago by genomax223k
4
votes
1
answer
137
views
1
answer
I want to know about the actual function of Bowtie?
... Hi friends, I am learning RNA_Seq. I want to know the actual function of bowtie. For my understanding bowtie takes reference genome file (.fa) as an input after that it generates .bt2 files as an output. In my point of view this step for indexing (string compression for aligning). Bowtie also used f ...
bowtie2 written 10 days ago by barrypraveen0 • updated 10 days ago by Brian Bushnell9.8k
0
votes
1
answer
143
views
1
answers
Comment: C: RNA-Seq tophat command error?
... Ok. Thank you very much ...
written 13 days ago by barrypraveen0

Latest awards to barrypraveen

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1731 users visited in the last hour