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Search: Posts Made By: bioenvisage
Forum: Bioinformatics 01-01-2011, 11:01 AM
Replies: 0
Views: 2,517
Posted By bioenvisage
SNP density

Can any one tell me how to calculate the SNP density for the SNPs identified from unigene sequences?

thanks
Forum: Bioinformatics 09-28-2010, 02:55 AM
Replies: 0
Views: 1,242
Posted By bioenvisage
SAM ro SOAP

hello,

Can any tell is there nay tool available to convert sam to soap output format.

thanks
Forum: Bioinformatics 09-24-2010, 06:54 AM
Replies: 292
Views: 161,306
Posted By bioenvisage
Hi Ih3, Is there any...

Hi Ih3,

Is there any utility/script/tool for converting SAM format to SOAP alignment output format.Iam using SOAPsnp which accepts only the SOAP aligner format.
Forum: Bioinformatics 09-24-2010, 12:48 AM
Replies: 2
Views: 2,710
Posted By bioenvisage
re

hi could you post ur script
Forum: Bioinformatics 09-23-2010, 05:17 AM
Replies: 2
Views: 2,710
Posted By bioenvisage
SAM to SOAP

Hello,

Can any one tell me how to convert SAM to SOAP output format, to use with the SOAPsnp.
Forum: Bioinformatics 08-06-2010, 06:06 AM
Replies: 1
Sam
Views: 1,466
Posted By bioenvisage
Sam

Hello,

Ia there any tool to convert SAM format to SOAPaligner output format.

thanks

karthik
Forum: Bioinformatics 04-15-2010, 01:21 PM
Replies: 4
Views: 1,627
Posted By bioenvisage
1x assembly

Hi,any one have experience of denovo asembly of solexa reads having 1x coverege by using velvet.
Forum: Bioinformatics 04-07-2010, 11:32 AM
Replies: 14
Views: 9,274
Posted By bioenvisage
hi the read order is in 0/1 0/2 0/1 ...

hi the read order is in

0/1
0/2
0/1
0/2
0/1
0/2
Forum: Bioinformatics 04-06-2010, 07:03 AM
Replies: 14
Views: 9,274
Posted By bioenvisage
hi maubp .. there are around 50 million reads

hi maubp .. there are around 50 million reads
Forum: De novo discovery 04-06-2010, 03:13 AM
Replies: 12
Views: 9,170
Posted By bioenvisage
velvet N50

Hi ,Iam working with velvet denovo assembly of illumina reads.Initially i trimmed the raw reads of illumina based on quality and after running the velvet with the subset of the reads the N50 is...
Forum: Bioinformatics 04-01-2010, 04:27 AM
Replies: 14
Views: 9,274
Posted By bioenvisage
Hi It is in one single file having forward and...

Hi It is in one single file having forward and reverse (1 & 2)
Forum: Bioinformatics 03-31-2010, 01:58 PM
Replies: 14
Views: 9,274
Posted By bioenvisage
removal of unpaired reads

Hi I would like to know is there any tool for removing the unpaired fastq reads from a huge set of paired end fastq data?
Forum: Bioinformatics 03-24-2010, 02:34 PM
Replies: 6
Views: 2,878
Posted By bioenvisage
re

hello zingster ..iam very new to this kind of research and iam not expertise like you in bioinfo ....so only i have these kind of questions araises..im sry if iam hard..
Forum: Bioinformatics 03-24-2010, 09:56 AM
Replies: 6
Views: 2,878
Posted By bioenvisage
number of contigs in velvet

hi all , what is the approximate total number of contigs we should get in a velvet assembly? I would like to know this because i did assemblies with various parameters but i always get more then...
Forum: Bioinformatics 03-22-2010, 12:09 PM
Replies: 7
Views: 2,268
Posted By bioenvisage
hi zingster and nicklomen .. thanx for your...

hi zingster and nicklomen .. thanx for your replies ..it was very use full .. My idea to validate is, if we have the sanger sequences of the species what we are assembling then we can do a blast...
Forum: Bioinformatics 03-22-2010, 03:47 AM
Replies: 7
Views: 2,268
Posted By bioenvisage
reg the validation of velvet assembly

Hi i did velvet denovo assembly for a species which does not have its previous genome information , so how can I validate my assembly?
Forum: Bioinformatics 03-21-2010, 02:18 PM
Replies: 3
Views: 2,827
Posted By bioenvisage
hi ,thanks for your reply...From the manual it is...

hi ,thanks for your reply...From the manual it is stated that with reference to the graph the expected cov is calculated as 14x ,so what i understood is we should take the value of the highest...
Forum: Bioinformatics 03-21-2010, 12:43 PM
Replies: 3
Views: 2,827
Posted By bioenvisage
velvet expected cov

Can any one tell how to set the expected coverege parameter in velvet denovo assembly , if i have the illumina reads of 0.1x cov.
Forum: Bioinformatics 02-16-2010, 08:10 AM
Replies: 1
Views: 1,386
Posted By bioenvisage
velvet

Hi .. ..If the velvet denovo assembly was done with contamination (chloroplast sequences ), the N50 is aboout 15 times higher than the assembly with out chloroplast sequences.I was trying to find out...
Forum: General 02-15-2010, 07:38 AM
Replies: 1
Views: 1,556
Posted By bioenvisage
tool for plotting

Hi , I would like to know is there any user friendly tool for plotting the assembly and alignment data other than R.

thanks
Forum: De novo discovery 02-13-2010, 05:05 PM
Replies: 4
Views: 3,165
Posted By bioenvisage
hi zingster thnx for ur reply ...but my read...

hi zingster thnx for ur reply ...but my read length is 75 bp, do u think it should be trimmed further.
Forum: De novo discovery 02-12-2010, 10:43 AM
Replies: 5
Views: 3,905
Posted By bioenvisage
ya the only way is u have to test run with small...

ya the only way is u have to test run with small data set by using different parameters and alos try to check these assemblies by using a denovo assembly viewer and then you can get an idea regarding...
Forum: De novo discovery 02-12-2010, 08:12 AM
Replies: 4
Views: 3,165
Posted By bioenvisage
velvet

hi After running velvet assembly I got Estimated Coverage = 25.12000
Estimated Coverage cutoff = 10.250000
Final graph has 11106 nodes and n50 of 498, max 13308, total 243547, using 221137/2500000...
Forum: De novo discovery 02-12-2010, 08:05 AM
Replies: 5
Views: 3,905
Posted By bioenvisage
velvet

You can try with plotting in R, look the velvet manual (choice of coverege cutoof).
Forum: De novo discovery 02-11-2010, 07:54 AM
Replies: 2
Views: 2,281
Posted By bioenvisage
velvet denovo

Hi ..I was running velvetg with various parameters but for different coverege cutoff iam getting the different results...how to optimize the coverege cutoff ..


thanks
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