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Forum: RNA Sequencing 08-11-2015, 07:37 AM
Replies: 5
Views: 2,577
Posted By konika
Thanks, it was actually old version of tophat...

Thanks, it was actually old version of tophat that also needs an input read to create transcriptome indexes.
Forum: RNA Sequencing 08-11-2015, 06:48 AM
Replies: 5
Views: 2,577
Posted By konika
tophat not creating transcriptome indexes

Hi
In my case The following command doesnt start tophat2. tophat2 just shows me the available options, like I have used a wrong option somewhere. Does anyone has an idea whats wrong here
The...
Forum: RNA Sequencing 08-11-2015, 05:51 AM
Replies: 1
Views: 841
Posted By konika
tophat2 transcriptome data files created

Hi I am providing tophat with pre-built bowtie index files, Gff files and the whole genome fasta file, but it still creates transcriptome data files and is building bowtie indexes. Is it necessary,...
Forum: RNA Sequencing 02-02-2015, 05:23 AM
Replies: 0
Views: 1,038
Posted By konika
Warnings in cuffdiff subsequently killing the program

Hi
I have run the command
cuffdiff -o /wrk/sushilth/analysis/differential_expression/all_samples_redo_cuffmerge2 \
-b...
Forum: RNA Sequencing 10-15-2014, 07:14 AM
Replies: 5
Views: 4,946
Posted By konika
Thanks, I used the older version of samtools and...

Thanks, I used the older version of samtools and it fixed.
Forum: RNA Sequencing 10-15-2014, 02:53 AM
Replies: 5
Views: 4,946
Posted By konika
Tophat error about samtools version

Hi
I have tried using tophat2 but still got a similar error
tophat2 -r 20 test_ref reads_1.fq reads_2.fq

[2014-10-15 12:50:45] Beginning TopHat run (v2.0.11)...
Forum: Bioinformatics 05-26-2014, 05:46 AM
Replies: 11
Views: 2,766
Posted By konika
I solved the memory thing, It was due to the...

I solved the memory thing, It was due to the wrong genome size.
The size should be in megabases so 2.8. Will post if I get useful result from VelvetOptimiser. Thanks
Forum: Bioinformatics 05-26-2014, 04:41 AM
Replies: 11
Views: 2,766
Posted By konika
Hi, I describe the Kmer coverage calculation...

Hi, I describe the Kmer coverage calculation above in the first post. This result was from a subsample of total reads. Yes,it is quite high coverage, waiting for velvetOptimiser to run.
Forum: Bioinformatics 05-26-2014, 04:38 AM
Replies: 11
Views: 2,766
Posted By konika
Hi, Yes I am using just one set of paired end...

Hi, Yes I am using just one set of paired end reads, will try with correct command and add 'CATEGORIES=1' there. New command will be :


VelvetOptimiser.pl -s 75 -e 159 -t 1 -f '-shortPaired...
Forum: Bioinformatics 05-26-2014, 02:25 AM
Replies: 11
Views: 2,766
Posted By konika
Apart from this, I run velvetg on the subsample...

Apart from this, I run velvetg on the subsample for Kmer hash 75-151, and kmercov 320-370 for each kmer length. I then compare all results for n50. Below is the result:
file n50 total.length...
Forum: Bioinformatics 05-26-2014, 02:21 AM
Replies: 11
Views: 2,766
Posted By konika
Hi, I have tried using subsample (40% of original...

Hi, I have tried using subsample (40% of original number of reads) and run VelvetOptimiser on it, but get the result
Velvet details:
Velvet version: 1.2.08
Compiled categories: 10
Compiled...
Forum: Bioinformatics 05-20-2014, 06:05 AM
Replies: 11
Views: 2,766
Posted By konika
Question Is high Kmer coverage in PE reads, good?

Hi
I am doing de novo assembly of a bacterial genome, through paired end reads using velvet.
If I use Kmer length 75, in the Kmer coverage formula along with other parameters I get:

Ck = C * (L...
Forum: Bioinformatics 04-28-2014, 04:13 AM
Replies: 2
Views: 771
Posted By konika
Question Identifying the type of sequencing from a SFF file

Hi
I have a very basic question,
I have a .SFF file. I know its not paired end reads data, but I was wondering how can I get more information from it such as : which type of sequencing is it? ...
Forum: Bioinformatics 10-07-2010, 02:06 AM
Replies: 24
Views: 11,938
Posted By konika
Hi, I have miRNA data and have aligned the...

Hi,
I have miRNA data and have aligned the nonredundant sequences for each of 3 samples to each of 5 chromosomes in Arabidopsis.
question -is it correct ? or should I use all sequences to map...
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