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Search: Posts Made By: Pinal
Forum: Bioinformatics 12-14-2015, 12:35 AM
Replies: 1
Views: 2,132
Posted By Pinal
Did you get your answer? I had the same...

Did you get your answer?

I had the same isuue. just solved it.
Forum: Bioinformatics 12-11-2015, 09:16 PM
Replies: 2
Views: 2,314
Posted By Pinal
cummeRbund readCufflinks Error in sqliteSendQuery

Dear All,

When using library cummeRbund with readCufflinks, I got errors:


Creating database /home/NGS/diff_out/cuffData.db
Reading Run Info File /home/NGS/diff_out/run.info
Writing runInfo...
Forum: RNA Sequencing 12-11-2015, 01:22 AM
Replies: 4
Views: 1,378
Posted By Pinal
thank for your reply blancha

thank for your reply blancha
Forum: RNA Sequencing 12-11-2015, 12:56 AM
Replies: 4
Views: 1,378
Posted By Pinal
thank for your reply blancha ...

thank for your reply blancha

Read_groups.info contains...

file condition replicate_num total_mass norm_mass internal_scale external_scale...
Forum: RNA Sequencing 12-10-2015, 10:38 PM
Replies: 4
Views: 1,378
Posted By Pinal
Post Replicates error in CummeRbund package in R

Dear All,

I am analyzing RNAseq data to study DEGs in two diffrent conditions. i don't have any replicate for my samples. tophat->cufflinks->cuffdiff pipeline is completed and now i want to plot...
Forum: Bioinformatics 03-18-2015, 10:54 PM
Replies: 8
Views: 1,838
Posted By Pinal
Thank you all. I think i have to go for SGA...

Thank you all.

I think i have to go for SGA or minia due to lack of memory. is it a good option to use paired end reads for assembly and then go for scaffolding with mate pair data.?
which tool...
Forum: Bioinformatics 03-17-2015, 01:06 AM
Replies: 8
Views: 1,838
Posted By Pinal
Thank you sarvidsson, I have access to 96GB...

Thank you sarvidsson,

I have access to 96GB memory and 24 core machine. is it sufficiant to work with Allpaths-LG?
Forum: Bioinformatics 03-16-2015, 11:58 PM
Replies: 8
Views: 1,838
Posted By Pinal
large genome assembly using paired end and mate paire reads.

Which assembler should i go for if i want to assemble genome of 1 -1.5 GB size. i have illumina paired end and mate pair reads of 101 bp length. how can i use mate paire reads for Scaffolding?
Forum: Bioinformatics 03-12-2013, 02:06 AM
Replies: 2
Views: 2,217
Posted By Pinal
How to extract unmapped reference sequence from BAM/SAM file.?

How to extract unmapped region from reference sequence from SAM/BAM file.?
Forum: Bioinformatics 12-07-2012, 06:26 AM
Replies: 0
Views: 924
Posted By Pinal
SNP filter using varFilter -D -d

varFilter -D -d (read depth) usage..

how to calculate average read depth..?? As sam tool suggest that The -D option of varFilter controls the maximum read depth, which should be adjusted to about...
Forum: Bioinformatics 09-26-2012, 11:00 AM
Replies: 2
Views: 1,212
Posted By Pinal
velvet assembly - getting more number of supercontigs than genes present

Does number of supercontigs matters for assembly.? i got a 40 MB fungal genome sequence assembly with ~12500 supercontigs by velvet software.?( more than no. of genes present) how can i validate it?
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