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Forum: Pacific Biosciences 04-03-2015, 01:36 AM
Replies: 5
Views: 3,611
Posted By bioman1
Thank you for all replying. If I have 1x PacBio,...

Thank you for all replying. If I have 1x PacBio, does it help to map my illumina reads and I have some transcriptome dataset to this PacBio assembly and get organelle contigs (mitochondria and...
Forum: Pacific Biosciences 03-27-2015, 02:08 AM
Replies: 5
Views: 3,611
Posted By bioman1
Improving assembly with PacBIo

We have one paired-end (2x 101 bp)libray Whole gnome short sequence (WGS) sequenced through illumina hiseq 2000. We have assembled genome assembly with Abyss software. The assembly has lower N50...
Forum: Bioinformatics 12-18-2014, 01:45 AM
Replies: 4
Views: 2,659
Posted By bioman1
SSR from denovo assembled genome

I am interested in finding SSR markers in our recently sequenced plant genome. Our plant genome is non-model and it is tetraploid. It was sequenced in hiseq2000 of one paired-end library of 101bp...
Forum: Bioinformatics 11-26-2014, 10:46 PM
Replies: 1
Views: 1,709
Posted By bioman1
Repeatmasker - suggestion

I am running repeat masker on a server, but it was failed in between when there was power shut down. Do you know the command to start again from where it ended.

I ran repeat masking with default...
Forum: Bioinformatics 11-19-2014, 04:43 AM
Replies: 6
Views: 1,966
Posted By bioman1
Thanks all for your suggestion. When I map my...

Thanks all for your suggestion. When I map my reads to denovo assembled genome (nuclear+mito) i get around 5x coverage.

Also, I tried by mapping my reads to reference mitochondria genome and I...
Forum: Bioinformatics 11-18-2014, 12:11 AM
Replies: 6
Views: 1,966
Posted By bioman1
Suggestion for mitochondrial genome assembly

1.I have denovo assembled my illumina paired-end reads (2x101 bp with abyss genome assembler and got contigs.
2.I have blasted my denovo assembled contig assembly against my closest reference...
Forum: Ion Torrent 11-04-2014, 01:48 AM
Replies: 10
Views: 7,117
Posted By bioman1
I should give no.of mapped bases instead of...

I should give no.of mapped bases instead of reads..my mapped reads is 9,055,285,852 bp on a on a 1491942955 bp assembly gives ~6X. But my question before assembling I get coverage I get around 20X...
Forum: Ion Torrent 11-03-2014, 01:44 PM
Replies: 10
Views: 7,117
Posted By bioman1
Sorry for making confusion. In my first...

Sorry for making confusion.

In my first post, the genome size is estimated by k-mer method (kmergenie), so the estimated genome size is around 2032558240 bp. The filtered reads assessed by fastqc...
Forum: Bioinformatics 11-03-2014, 12:17 PM
Replies: 9
Views: 2,058
Posted By bioman1
Thanks SES. I will try and I will contact you if...

Thanks SES. I will try and I will contact you if any difficulties.
Forum: Ion Torrent 11-03-2014, 12:06 PM
Replies: 10
Views: 7,117
Posted By bioman1
Thanks Brian. Our plant is tetraploid genome. ...

Thanks Brian. Our plant is tetraploid genome.

Mapped sequence evaluated by qualimap (http://qualimap.bioinfo.cipf.es/)
Reference size (bp)- 1491942955
No.of mapped reads(bp) 102,654,077-...
Forum: Ion Torrent 11-03-2014, 01:00 AM
Replies: 10
Views: 7,117
Posted By bioman1
We have done WGS using illumina paired-end...

We have done WGS using illumina paired-end sequencing (Hi seq). After pre-processing, we got 42300018262 bases, mean read length is 101 bp
and genome size is 2032558240 bp. Then I get coverage...
Forum: Bioinformatics 10-31-2014, 10:49 PM
Replies: 9
Views: 2,058
Posted By bioman1
Thank you all for suggestiona. We have budget...

Thank you all for suggestiona. We have budget constraint, we can proceed gor further funding by making one publication with available data. Do I open to any kind of suggestind.
SES please let me...
Forum: Bioinformatics 10-30-2014, 06:54 AM
Replies: 9
Views: 2,058
Posted By bioman1
Making sense of low coverage plant genome

In our lab we have de novo assembled non-model plant WGS ( 1 paired-end library - 2x101 bp) of insert size 240 bp, with N50 around 1 kbp. The estimated genome size is around
2GB. Through read...
Forum: Bioinformatics 10-28-2014, 09:50 PM
Replies: 0
Views: 1,161
Posted By bioman1
expectation of contig and scaffold length

I have assembled Illumina paired-end reads (2X101 bp) of one library of insert size 240 bp of WGS of polyploid plant sequences . I have obtained around contig N50 1 Kbp. My estimated genome size is...
Forum: Bioinformatics 09-30-2014, 08:09 PM
Replies: 1
Views: 2,100
Posted By bioman1
Exclamation RepeatMasker-help

I would like to use repeatmasker to identify repetitive element in my de novo assembled genome. I have installed repeatmasker with repbase database in my local server.

My de novo assembled genome...
Forum: Bioinformatics 09-28-2014, 10:24 PM
Replies: 2
Views: 2,085
Posted By bioman1
Repeat sequences-Genome assembly

I have WGS sequence of illumina paired-end reads (2x101 bp) of the plant crop. I have de novo assembled the reads using velvet.

I would like to do two things

1. To do de novo genome assembly...
Forum: Bioinformatics 09-28-2014, 06:52 AM
Replies: 1
Views: 1,933
Posted By bioman1
Script to extract contigs based on sequence size

Do you anyone have script or you know any script available already to read the nucleotide fasta file and extract the contigs based on sequence size (eg.300 bp, 500 bp, 1 Kbp etc).
Forum: Bioinformatics 09-24-2014, 11:46 PM
Replies: 24
Views: 14,998
Posted By bioman1
I have tried MITObim tool to extract mtgenome, I...

I have tried MITObim tool to extract mtgenome, I got lot of gaps in mtgenome assembly. So I tried to do de novo assembly of my WGS data and extract mtcontigs through blast. Below are the steps

1.I...
Forum: Bioinformatics 09-15-2014, 01:54 AM
Replies: 18
Views: 7,759
Posted By bioman1
@WhatsoEver. Thanks for your suggestion. ...

@WhatsoEver. Thanks for your suggestion.

1.My crop is non-model. I don't know the close relative crop species.
2. I have only WGS sequence with one paired end for each variety with same insert...
Forum: Bioinformatics 09-11-2014, 11:41 PM
Replies: 18
Views: 7,759
Posted By bioman1
Lol..I didn't it is a prank script.. I have...

Lol..I didn't it is a prank script..

I have another sequence using a whole-genome shotgun strategy of illumina paired-end reads, but this sequence from
another variety belong the same crop. (say...
Forum: Bioinformatics 09-04-2014, 08:11 PM
Replies: 18
Views: 7,759
Posted By bioman1
My plant is allotetraploid crop. Sequenced...

My plant is allotetraploid crop. Sequenced through Hiseq, illumina paired-end reads of 101 bp length.

I tried with different Kmer 41 (which was estimated by SGA preqc) and assembled with Minia...
Forum: Bioinformatics 09-02-2014, 04:58 AM
Replies: 18
Views: 7,759
Posted By bioman1
Thanks luc & WhatsOEver for your comments. The...

Thanks luc & WhatsOEver for your comments. The difficulty in my genome assembly, my plant is a tetraploid crop and highly heterozygous. Also non-model crop and my coverage of my sequence around 5x.
Forum: Bioinformatics 09-01-2014, 06:18 PM
Replies: 18
Views: 7,759
Posted By bioman1
I did CEGMA completness test. I have very low...

I did CEGMA completness test. I have very low coverage genome around 5x. The CEGMA completness test is around 20%, is this metric OK for publication?

# Statistics of the completeness of the...
Forum: Bioinformatics 09-01-2014, 05:01 AM
Replies: 1
Views: 1,384
Posted By bioman1
Lightbulb running CEGMA VM

I used CEGMA VM on windows 7 Operating system. I used virtual box for VM and followed steps as in:http://korflab.ucdavis.edu/datasets/cegma/cegma_vm.html


CEGMA did run successfully, but it does...
Forum: Bioinformatics 08-27-2014, 08:01 PM
Replies: 3
Views: 1,775
Posted By bioman1
Unhappy Trouble running CEGMA sample data

Hello,

I am installing cegma for the first time and I am having trouble running sample data. I googled it, I could not able to find a solution. I followed steps exactly as described in...
Showing results 1 to 25 of 80

 


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