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Forum: RNA Sequencing 08-02-2018, 07:07 PM
Replies: 0
Views: 1,236
Posted By znasim09
Question Can the "QNAME" information of a SAM file be used for estimate uniquely mapped reads?

Hello everyone,

First of all, I know there has been a lot of discussions related to uniquely mapped reads estimation (sorry for bringing it up again).

My question is that QNAME, the first...
Forum: Bioinformatics 12-18-2016, 04:44 PM
Replies: 0
Views: 1,844
Posted By znasim09
Intron retention events with AStalavista

Hello everyone,

I am using AStalavista for detecting splicing events in RNA-seq data of my Arabidopsis mutants. I found differences in intron retention between wild type and mutants.

My...
Forum: Bioinformatics 12-02-2016, 11:32 PM
Replies: 1
Views: 2,763
Posted By znasim09
cummeRbund Error: This data.table install has not detected OpenMP support

Hello everyone,
I have been using R package "cummeRbund" for a while now (with not much of knowledge though), however, its until very recently that I am getting an error

"This data.table install...
Forum: Bioinformatics 09-12-2016, 08:51 PM
Replies: 5
Views: 1,887
Posted By znasim09
@thermophile, I made the heatmap using...

@thermophile,
I made the heatmap using csHeatmap(myGenes,cluster='both') command. So how can I modify it to get clear differentiation of the expression pattern in different groups/samples in terms...
Forum: Bioinformatics 09-09-2016, 06:19 PM
Replies: 5
Views: 1,887
Posted By znasim09
Question Highlighting genes of interest in RNA-seq heatmap

Hello everyone,

I was wondering whether its possible to make a heat map from cuffdiff output that highlights a few genes in a different color (or any other way). E.g., if I want to highlight 5-7...
Forum: RNA Sequencing 08-23-2016, 05:45 PM
Replies: 0
Views: 1,632
Posted By znasim09
spliceR: problems in detecting NMD sensitivity from RNA-seq data

Hello everyone,

I want to detect the NMD sensitivity from RNA-seq data of my Arabidopsis mutants. I read that spliceR can be used for this. However, spliceR requires CDs from UCSC, that does not...
Forum: Bioinformatics 08-11-2016, 05:10 PM
Replies: 5
Views: 1,640
Posted By znasim09
Hey Tristan, Thanks for the time. I said I am...

Hey Tristan,
Thanks for the time. I said I am not a bioinformatician but I am not that bad in installing and executing programs. Can you mention the programs/steps that I need to do? I am pretty...
Forum: Bioinformatics 08-10-2016, 04:21 PM
Replies: 5
Views: 1,640
Posted By znasim09
Thanks Tristan for your reply. But as I am not a...

Thanks Tristan for your reply. But as I am not a bioinformatician, could you be a bit simpler? I didn't understand much :(
Forum: Bioinformatics 08-10-2016, 03:12 AM
Replies: 5
Views: 1,640
Posted By znasim09
Smile How to find Trans gene integration position in the genome?

Hello everyone,

I was wondering how can I find where my gene of interest is integrated in the Arabidopsis genome? I have the genome sequence data for the transgenic line expressing my gene of...
Forum: RNA Sequencing 08-08-2016, 11:32 PM
Replies: 1
Views: 1,250
Posted By znasim09
Post Alternative splicing summary from Cuffdiff output

Hello everyone,
I want to get a kind of summarized results for all the Alternative splicing events from the Cuffdiff output,
like, sample 1 = 1030 IR events, 1200 ES events
...
Forum: Illumina/Solexa 04-11-2016, 04:25 AM
Replies: 4
Views: 6,176
Posted By znasim09
@dschika will it then give vcf format output? ...

@dschika will it then give vcf format output?

@GenoMax,

I am using bwa-0.7.13 and
samtools-1.3
Forum: Illumina/Solexa 04-11-2016, 12:46 AM
Replies: 4
Views: 6,176
Posted By znasim09
Samtools mpileup error "[W::sam_read1] parse error at line 1"

Hello everyone,

I am analyzing WGS data of my mutant (Raw data in fastq), I performed the alignment by using Bowtie and BWA as:

Using Bowtie:
bowtie -S reference.fa file.sam
then converted...
Forum: SOLiD 04-08-2016, 08:56 PM
Replies: 13
Views: 6,212
Posted By znasim09
Hey mastal, I used this command: bowtie -f -C...

Hey mastal,
I used this command:
bowtie -f -C a_thaliana test_F3.csfasta -Q test_F3_QV.qual > out_F3.sam

But still I am getting the same results (Only 13% mapping)

# reads processed: 6221913...
Forum: SOLiD 04-08-2016, 01:39 AM
Replies: 13
Views: 6,212
Posted By znasim09
I tried to add the qual file by using this...

I tried to add the qual file by using this command:
perl bowtie -f -C -Q test_F3.csfasta a_thaliana test_F3_QV.qual > out_F3.sam

But it gave the following info:

Warning: could not parse...
Forum: SOLiD 04-07-2016, 10:54 PM
Replies: 13
Views: 6,212
Posted By znasim09
Hey mastal, I color indexed the reference...

Hey mastal,

I color indexed the reference genome with the command

perl bowtie-build --wrapper basic-0 -C /Users/znasim09/Documents/Perl_packages/bowtie-1.1.2/genomes/Ath_reference.fa ...
Forum: SOLiD 04-07-2016, 02:15 AM
Replies: 13
Views: 6,212
Posted By znasim09
@Mastal I read colorspace alignment section...

@Mastal
I read colorspace alignment section quite a few times but couldn't understand it properly :( . The data I want to analyze is single end.
I downloaded the SRA file and converted it to...
Forum: SOLiD 04-07-2016, 01:40 AM
Replies: 13
Views: 6,212
Posted By znasim09
@dpryan Thanks for the reply. I indexed...

@dpryan
Thanks for the reply.
I indexed Arabidopsis genome using the script "make_a_thaliana_tair,sh"
But, There are plenty of options that I couldn't understand (as I am a beginner). Can you...
Forum: SOLiD 04-06-2016, 09:30 PM
Replies: 13
Views: 6,212
Posted By znasim09
Unhappy Any video tutorial for alignment of csfasta and qual files?? Or its fastq conversion?

Hello everyone,

For the last few days I have been searching different forums to understand converting csfasta and qual files to fastq and/or to align the files. But due to limited (or I can say no...
Forum: RNA Sequencing 09-11-2015, 10:49 PM
Replies: 0
Views: 1,112
Posted By znasim09
Error in (Gviz) genetrack<-makeGeneRegionTrack(myGene)

Hi,
I am unable to use the Gviz genetrack. When i try, it gives me the error (Error in grid.Call.graphics(L_setviewport, vp, TRUE) :
non-finite location and/or size for viewport)

Details are...
Forum: RNA Sequencing 09-09-2015, 12:22 AM
Replies: 0
Views: 1,285
Posted By znasim09
Red face Problem with readcufflinks and Gene Feature plots

I am new to RNA seq analysis, need help in fixing these problems:

First, when i am trying to readcufflinks commond i get these errors:

> library(cummeRbund)
Loading required package:...
Forum: Bioinformatics 09-04-2015, 03:44 AM
Replies: 4
Views: 1,596
Posted By znasim09
What about Arabidopsis ?? It's genome is not...

What about Arabidopsis ?? It's genome is not included in the UCSC
Forum: Bioinformatics 09-03-2015, 11:55 PM
Replies: 4
Views: 1,596
Posted By znasim09
Hey anyone solved this issue? Me too having the...

Hey anyone solved this issue? Me too having the same problem...
Forum: Bioinformatics 09-02-2015, 10:00 PM
Replies: 14
Views: 9,611
Posted By znasim09
Hey Gonza, were you able to solve this problem? I also have the same problem

Hey Gonza, were you able to solve this problem? I also have the same problem
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