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Search took 0.01 seconds. Search: Posts Made By: ketan_bnf
Forum: Bioinformatics 10-07-2011, 11:15 PM
Replies: 6
Views: 2,705
Posted By ketan_bnf
Hi Peitx, Sequences may be of low quality...

Hi Peitx,

Sequences may be of low quality and/or small in length (<20 bp dufault). It is not necessary all sequences will be used for mapping to genome.

Regards,
Forum: 454 Pyrosequencing 09-13-2011, 10:14 PM
Replies: 1
Views: 1,472
Posted By ketan_bnf
Error in GSMapper output, 454Allcontigs.fna and 454NewblerMetrics.txt

Hi all,

I mappped reads to reference using GSMapper, it generated result files. When i see 454AllContigs.fna, it shows two contigs generated, first contig is of size 1155 nt numreads used to form...
Forum: Bioinformatics 09-12-2011, 05:29 AM
Replies: 2
Views: 2,171
Posted By ketan_bnf
Create one sequence based on overlapping primer sequences in amplicon

Hi all,

Recently we have carried out amplicon sequencing for metagenome. I want to create a single long sequence based on overlapping primers, so i can get whole gene. How can i accomplish this?...
Forum: Bioinformatics 09-11-2011, 11:33 PM
Replies: 6
Views: 26,174
Posted By ketan_bnf
You can use samtools mpileup option, visit this...

You can use samtools mpileup option, visit this link

http://samtools.sourceforge.net/mpileup.shtml

also you can use GATK for variant calling.
Forum: Bioinformatics 09-11-2011, 11:30 PM
Replies: 1
Views: 2,339
Posted By ketan_bnf
Starting cancer transcriptome analysis of 454 sequencing data

Hi all,

We have a cancer related transcriptome data which is sequenced using 454 GS-FLX titanium, for which reference genome is available.

I want to set work pipeline for bioinformatics...
Forum: 454 Pyrosequencing 07-25-2011, 04:05 AM
Replies: 1
Views: 1,920
Posted By ketan_bnf
gsRunBrowser not able to carry out full processing

Hi all,

We have cluster with configuration,
2.75 TB Harddisk
16 GB RAM
1 Head Node, 4 Sub Node each having two core2duo processor.

we recently carried out a run and facing a problem in...
Forum: Bioinformatics 07-20-2011, 10:00 PM
Replies: 0
Views: 1,431
Posted By ketan_bnf
amino acid change effect on protein structure using bioinformatics

Hi all,

I have 195 nsSNPs that will make amino acid change in protein sequence. I want to find whether thei'll effect protein structure/function? So far i have used Pmut and SNAP tools.

Is...
Forum: Bioinformatics 06-11-2011, 04:26 AM
Replies: 11
Views: 6,163
Posted By ketan_bnf
Want to create refGene.txt file for bacteria, problem compliling kent source

Hi all,

I want to create refGene.txt file to give as input in GS Reference Mapper as it only accepts annotation in this format.

So i downloaded kent source to make refGene.txt file, but the...
Forum: Bioinformatics 05-22-2011, 11:50 PM
Replies: 1
Views: 1,671
Posted By ketan_bnf
Need Help, gap between two contigs formed by mapping

Hi all,

I have mapped reads to a ref seq using gsMapper and formed a contigs, now i want to extract & count length of the gap in reference sequence where no reads have mapped

Ref seq :...
Forum: Bioinformatics 05-03-2011, 10:10 PM
Replies: 7
Views: 3,865
Posted By ketan_bnf
hi haonmada, have you read this, FAQ on...

hi haonmada,

have you read this, FAQ on http://bio-bwa.sourceforge.net/

according to bwa manual, for 454 reads you should use bwa bwasw, and for short reads less than 200 bp sensitivity is...
Forum: Bioinformatics 05-03-2011, 09:58 PM
Replies: 48
Views: 63,886
Posted By ketan_bnf
Hi blackgore, for your first question about...

Hi blackgore,

for your first question about Allele frequency, in vcf file AF1 is showing the Allele frequency for the related alt base.

read starting of the vcf file there are coments,
...
Forum: Bioinformatics 04-14-2011, 09:02 PM
Replies: 48
Views: 63,886
Posted By ketan_bnf
Hi! marcela, Thanks for pointing out an...

Hi! marcela,

Thanks for pointing out an error, my mistake in writing PL,

it should be like

(...) A T,G (...) DP=35;AF1=1;CI95=0.5,1;DP4=0,0,1,8;MQ=60 PL:GT:GQ 96,47,70,35,0,70:1/1:72
...
Forum: Bioinformatics 03-21-2011, 01:58 AM
Replies: 5
Views: 2,559
Posted By ketan_bnf
According to this...

According to this (http://contig.wordpress.com/2010/08/31/running-newbler-de-novo-transcriptome-assembly-i/) post isogroups contains isotigs which are formed from same contigs and also having...
Forum: Bioinformatics 03-20-2011, 11:38 PM
Replies: 5
Views: 2,559
Posted By ketan_bnf
thanks for reply natstreet I have done a...

thanks for reply natstreet

I have done a transcript assembly for transcriptome and formed isotigs. I am not much clear about isotig concept and also when analyzing isotig files, i can see just 4...
Forum: Bioinformatics 03-16-2011, 11:03 PM
Replies: 5
Views: 2,559
Posted By ketan_bnf
Finding Alternative splicing events from 454 transcriptome

Hi all.

I have transcriptome data from 454 sequencer. I have assembled it using de novo gsAssembler and formed a contigs (i am not using isotigs). I want to find alternative splicing events from...
Forum: Bioinformatics 03-03-2011, 01:13 AM
Replies: 8
Views: 5,272
Posted By ketan_bnf
Yes, i can see 'Zoom in to see alignments' after...

Yes, i can see 'Zoom in to see alignments' after loading .bam track to IGV

[orf@localhost q20]$ samtools tview GKUNU9Q04_chr1_q20_sort.bam chr1.fa

After applying this command in terminal i can...
Forum: Bioinformatics 03-02-2011, 11:50 PM
Replies: 8
Views: 5,272
Posted By ketan_bnf
Thanks for reply, i have used tablet to view...

Thanks for reply,

i have used tablet to view my bam alignment, can see alignments very well..

For samtools tview i have tried but the problem is it shows 'N' in my chromosome sequece instead of...
Forum: Bioinformatics 03-02-2011, 09:11 PM
Replies: 4
Views: 9,184
Posted By ketan_bnf
If you have vcf file and want to annotate SNP you...

If you have vcf file and want to annotate SNP you can use

1) EnsEMBL Variant effect predictor
2) snpEff software

both works with cow, accepts vcf file as input and gives GENEID, transcript...
Forum: Bioinformatics 02-25-2011, 10:54 PM
Replies: 1
Views: 7,578
Posted By ketan_bnf
pls visit...

pls visit http://seqanswers.com/forums/showthread.php?t=9345
Forum: Bioinformatics 02-25-2011, 10:49 PM
Replies: 8
Views: 5,272
Posted By ketan_bnf
NO, i have not zoomed the view. I am by default...

NO, i have not zoomed the view. I am by default just giving bam file as input, selecting chromosome sequence to which bam file has alignment record, after that no tracks are shown in the view area.
Forum: Bioinformatics 02-25-2011, 02:34 AM
Replies: 8
Views: 5,272
Posted By ketan_bnf
IGVtools 1.5 not showing bam alignments

Hi

I am using IGV 1.5 to view bam file, but i am not getting tracks in IGV. This is also happening with my vcf file. Why?

I ahve made idex for both the bam/vcf files FYI.
Forum: Bioinformatics 02-23-2011, 12:30 AM
Replies: 9
Views: 4,464
Posted By ketan_bnf
If you want to find SNPs, you should map reads to...

If you want to find SNPs, you should map reads to ref seq using gsMapper or map contigs to ref seq using BWA http://bio-bwa.sourceforge.net/, get output in sam, extarct SNPs using SAMTools,...
Forum: Bioinformatics 02-22-2011, 10:09 PM
Replies: 4
Views: 3,388
Posted By ketan_bnf
Sorry suninsky for posting in your thread, I...

Sorry suninsky for posting in your thread,

I am having 454 exome reads aligned to ref seq using bwa to sam file.
Is it possible to find reads spanning exon region?
Forum: Bioinformatics 02-22-2011, 08:55 PM
Replies: 9
Views: 4,464
Posted By ketan_bnf
Hi sulicon, Are you mapping contigs to the...

Hi sulicon,

Are you mapping contigs to the reference seq using gsMapper?

if your contigs are larger than 2000bp gsMapper will not consider them for mapping to the ref seq, as i got that error...
Forum: Bioinformatics 02-22-2011, 08:18 PM
Replies: 4
Views: 3,388
Posted By ketan_bnf
I am also finding a answer to this question, i am...

I am also finding a answer to this question, i am working on single end reads.

If somebody know about this please help.
Showing results 1 to 25 of 59
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