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Search: Posts Made By: meghavarshney
Forum: Bioinformatics 09-14-2016, 09:37 PM
Replies: 0
Views: 1,364
Posted By meghavarshney
Unhappy Uneak pipeline in gbsv2

Hello Everyone,

Currently I am Woking on the pipeline of GBSv2 and my query is regarding the same.
AS I am new to this field.
Currently I am facing problem with UNEAK pipeline on GBSv2.
So...
Forum: Bioinformatics 05-06-2016, 11:29 PM
Replies: 0
Views: 688
Posted By meghavarshney
pstacks software error

Hello everyone,
can you please tell me how to resolve it .

as i am working on Stacks tool here i am trying to run pstack , cstack and sstacks separately.
so i am getting this error ...
Forum: Bioinformatics 05-04-2016, 10:25 PM
Replies: 2
Views: 1,268
Posted By meghavarshney
as after your suggestion i tried to unable bam...

as after your suggestion i tried to unable bam file .
as i was not able to do this in a proper way, so i just tried to reinstall it
with these commands
[root@bioinfo3-c stacks-1.40]# ./configure...
Forum: Bioinformatics 05-01-2016, 09:06 PM
Replies: 2
Views: 1,268
Posted By meghavarshney
GBS:stakcs software error in ref_map.pl

Hello Everyone,

I am currently analysing GBS data using stacks software as i ma currently facing some problem with ref_map.pl.
According to this script not getting proper output for this run.
...
Forum: Bioinformatics 09-08-2015, 03:29 AM
Replies: 5
Views: 1,712
Posted By meghavarshney
Mr. Michael.Ante and Mr. Devon Ryan thanks a lot...

Mr. Michael.Ante and Mr. Devon Ryan thanks a lot for sharing this information.
Forum: Bioinformatics 09-07-2015, 02:49 AM
Replies: 5
Views: 1,712
Posted By meghavarshney
thanks for your reply , but i need to know about...

thanks for your reply , but i need to know about the main reason / logic behind this. And the other thing why am I getting 3' adapter seq in both reads( R1 and R2)???
Forum: Bioinformatics 09-07-2015, 02:44 AM
Replies: 1
pca
Views: 1,064
Posted By meghavarshney
pca

hello every one,
could you suggest me how to create 3d PCA plot with multivariate data as (need to plot PCA for samples not for genes)

example data:

Genename S1 S2 S3 S4 S5 S6 ...
Forum: Bioinformatics 09-03-2015, 04:12 AM
Replies: 5
Views: 1,712
Posted By meghavarshney
adapter contamination in reads?????

hello everyone,

I would like to ask one qus: why am I getting 3'adapter sequences in R1 and R2 reads (as according to seq protocol machine only generates seq of the fragment between...
Forum: Bioinformatics 08-10-2015, 09:41 PM
Replies: 1
Views: 1,475
Posted By meghavarshney
Question how to set one sample as a control for my other sample in gene differential analysis

Hello everyone
I have a question.I have 3 stages of 2 diff genotype from a single tissue type i would like to chk differential gene expression analysis among these genotype at different stage. but...
Forum: Bioinformatics 07-27-2015, 10:20 PM
Replies: 2
Views: 1,656
Posted By meghavarshney
actually i need to know correlation genewise not...

actually i need to know correlation genewise not samplewise so can you help me in that matter
Forum: Bioinformatics 07-20-2015, 12:48 AM
Replies: 2
Views: 1,656
Posted By meghavarshney
correlation analysis on gene basis

hello every one,

as i am learning RNA seq analysis so can anyone told m how to calculate correlation among 3 biological replicates on the basis of "gene and their fpkm".
Forum: Bioinformatics 07-03-2015, 04:04 AM
Replies: 2
Views: 2,058
Posted By meghavarshney
get resolved

this problem is also get resolved after i replace the older version of survival package wid the latest one
Old packages: 'survival'
Update all/some/none? [a/s/n]: a
trying URL...
Forum: Bioinformatics 07-03-2015, 03:58 AM
Replies: 7
Views: 2,098
Posted By meghavarshney
Smile thnkxx

thnkx to both of you . i got solution as for this i reinstalled HTSeq again as a regular user and now its properly working for me .


thankx again :)
Forum: Bioinformatics 07-02-2015, 08:44 PM
Replies: 7
Views: 2,098
Posted By meghavarshney
i had checked but still i didn't find ...

i had checked but still i didn't find
[pinky@localhost bin]$ htseq-count
bash: htseq-count: command not found...

as from root this folder contain
[root@localhost bin]# ls
annotateBed ...
Forum: Bioinformatics 07-02-2015, 04:58 AM
Replies: 7
Views: 2,098
Posted By meghavarshney
I had installed it in this location and still m...

I had installed it in this location and still m not able to access it
[root@localhost HTSeq-0.6.1]# python setup.py install --user
running install
running bdist_egg
running egg_info
writing...
Forum: Bioinformatics 07-02-2015, 04:45 AM
Replies: 2
Views: 2,058
Posted By meghavarshney
error in GenomicRanges package

hii everyone,

i was working with this package so i got some error
> library("GenomicFeatures")
> testFile <- system.file("bam", "accepted_hits.bam", package = "leeBamViews")
> aligns <-...
Forum: Bioinformatics 07-01-2015, 09:13 PM
Replies: 7
Views: 2,098
Posted By meghavarshney
Question error with htseq count and bed tool

hello every one,

as i am working on count based differential analysis and for that i am trying to use HTSEQ and bedtools
1. I am using Bedtool to count read in as

bedtools multicov -bams...
Forum: Bioinformatics 05-28-2015, 03:23 AM
Replies: 1
Views: 1,919
Posted By meghavarshney
csScatter: Error in match(x, table, nomatch = 0L)

hello everyone,

i am getting this error in csScatter command.

> csScatter(genes(cuff))
Error in match(x, table, nomatch = 0L) :
argument "x" is missing, with no default
Forum: Bioinformatics 05-11-2015, 09:49 PM
Replies: 4
Views: 1,246
Posted By meghavarshney
thanks a lot sir , But i wuold like to find...

thanks a lot sir ,
But i wuold like to find out correlation among two biological replicates at sequence level .. can we do that...
Forum: Bioinformatics 05-11-2015, 09:33 PM
Replies: 4
Views: 1,246
Posted By meghavarshney
thanks a lot sir , As may be I typed my...

thanks a lot sir ,
As may be I typed my question in a wrong way actually i would like to find out correlation between the two biological replicates at sequence level. can we do that.
One another...
Forum: Bioinformatics 05-11-2015, 04:08 AM
Replies: 4
Views: 1,246
Posted By meghavarshney
hello

hello every one ,

i am a beginner for rna seq analysis, i would like to know that how to perform sample comparison (how to compare two biological replicates/varieties). and how to use fastq file...
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