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Forum: General 09-21-2015, 02:35 AM
Replies: 0
Views: 1,254
Posted By mandar.bobade60
Structural variation detection from Exome-seq single-end data

Hi,
I am having single-end sequencing data from ION TORRENT which further subjected to reference alignment using Bowtie2. After that I ran GATK pipeline for SNP detection. Now I want to detect...
Forum: General 02-09-2015, 11:05 PM
Replies: 1
Views: 1,699
Posted By mandar.bobade60
Genome size estimation for paired end and mate paired data

Dear all,
I have paired end as well as mate paired data for de novo assembly. The data size of paired end data is around 91 GB and around 100GB for mate paired data. The read length is 101 nt for...
Forum: Bioinformatics 11-24-2014, 05:23 AM
Replies: 2
Views: 1,283
Posted By mandar.bobade60
It would be great if someone directs me on this...

It would be great if someone directs me on this query..
Forum: General 11-24-2014, 04:59 AM
Replies: 1
Views: 1,394
Posted By mandar.bobade60
Finding contaminant contigs in assembly

Hi,

I have generated plant mitochondrial assembly for which I would like to find contamination from chloroplast as well as nuclear genome. I have also run BlastN using same species nuclear genome...
Forum: Bioinformatics 11-21-2014, 04:01 AM
Replies: 2
Views: 1,283
Posted By mandar.bobade60
Singletons in De novo assembly

Hi,

I am doing de novo assembly for mitochondrial genome for that after being used Velvet and Amos(minimus2), I have got more of singletons than assembled sequences. So, around 5000 nucleotides...
Forum: General 11-19-2014, 08:56 PM
Replies: 4
Views: 4,022
Posted By mandar.bobade60
Thanks alot Brian once again for your comprensive...

Thanks alot Brian once again for your comprensive explanation. Further peaks, after first error and second actual, there are no apparent peaks. So, I assume whaterver first row volume is there, is my...
Forum: General 11-18-2014, 11:24 PM
Replies: 4
Views: 4,022
Posted By mandar.bobade60
Thanks Brian. It, BBMAP, did work well, since it...

Thanks Brian. It, BBMAP, did work well, since it gave volume in first row which is very much near to my specie's nearby species' genomic size unlike jellyfish. Only thing is I had to subsample my...
Forum: General 11-18-2014, 04:32 AM
Replies: 4
Views: 4,022
Posted By mandar.bobade60
Unhappy Genome size estimation for paired end data

Hi,

I am working with Illumina paired-end data with read length (l) 101 to generate de novo assembly. I am trying to predict genome size as per given formula, M = N * (L-K+1)/L.
The M value I...
Forum: Bioinformatics 10-28-2014, 04:08 AM
Replies: 46
Views: 16,342
Posted By mandar.bobade60
Smile Please set the Path using...

Please set the Path using setwd("wherever/ur/cuffdiff/result/is") in R
And check once again.
I had got same even though I had mentioned path with:

cuff <-...
Forum: General 10-22-2014, 02:46 AM
Replies: 1
Views: 1,546
Posted By mandar.bobade60
de novo assembly for mitochondrial genome

Hi all,
I am working first time on de novo assembly. I am working on mitochondrial genome assembly of plant species. My expected genome size is about ~800KB and after velvet+AMOS use it is coming...
Forum: Bioinformatics 09-23-2014, 02:54 AM
Replies: 5
Views: 2,823
Posted By mandar.bobade60
Subsampling

Dear Brian Bushnell,
I did subsampling and after subsmapling N50 value is getting substantially increased.
I have 101300000 reads with expected mitochondrial genome size of 715000 base pairs.
But...
Forum: Bioinformatics 09-16-2014, 02:59 AM
Replies: 5
Views: 2,823
Posted By mandar.bobade60
Thank you WhatsOEver for your paper link. ...

Thank you WhatsOEver for your paper link.

It's only mitochondrial data with 24GB for each end, so collectively 48GB. But coverage is huge thats why data is too much. The only filtering are done...
Forum: Bioinformatics 09-15-2014, 07:29 AM
Replies: 5
Views: 2,823
Posted By mandar.bobade60
de novo assembly using velvet and Amos

Hi all,

I am newbie in NGS data analysis and first task in it come to me is de novo assembly. I have plant mitochondrial genome to assemble for which I have almost 24GB of data with R1 and R2...
Forum: Introductions 09-01-2014, 10:39 PM
Replies: 1
Views: 839
Posted By mandar.bobade60
Hi, This is Mandar from India. Currently...

Hi,
This is Mandar from India. Currently working as a data scientist. Newbie to NGS data hope to have cooperation.
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