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Forum: Bioinformatics 07-12-2012, 09:08 PM
Replies: 4
Views: 1,962
Posted By genelab
thanks for you reply~ my purpose is to...

thanks for you reply~

my purpose is to obtain the deleterious snp sits.

Any body knows ?


Many thanks~
Forum: Bioinformatics 07-12-2012, 07:11 PM
Replies: 4
Views: 1,962
Posted By genelab
Smile Deleterious information in dbSNP

Hello everyone,
How could I obtain the SNPs which are deleterious in the dbSNP?

Is the recent versions of dbSNP containing the deleterious information if the SNP sites is deleterious?


Thanks...
Forum: Bioinformatics 04-10-2011, 05:59 PM
Replies: 4
Views: 2,988
Posted By genelab
It seems that some problems exist in your gdb...

It seems that some problems exist in your gdb from the warning message "shared library handler failed to enable breakpoint". I am sorry I didn't encounte this kind of error message before and cannot...
Forum: Bioinformatics 04-08-2011, 06:14 PM
Replies: 4
Views: 2,988
Posted By genelab
We once run into this error, when we run the...

We once run into this error, when we run the Soap2.2. We used gdb to debug the error, and we found it is the libstd++.so library which was not compatible with the Soap2.20 executable program. I just...
Forum: Bioinformatics 01-30-2011, 09:41 PM
Replies: 2
Views: 3,142
Posted By genelab
Find SNP in Sanger sequenced gene

Hi guys,
I have about 120 sequences of the same genes from our sample, which are sequenced by Sanger methods, How can I get the SNP sites among this gene compared to the reference gene? Is there...
Forum: Bioinformatics 12-09-2010, 10:24 PM
Replies: 0
Views: 1,771
Posted By genelab
building unigene form contigs

Hi guys,
Can someone give me any suggestions how to get the unigene from the contigs assemblied form the RNA-Seq short reads?
Thanks!:)
Forum: Bioinformatics 09-18-2010, 01:25 AM
Replies: 5
Views: 9,211
Posted By genelab
Zigster, thanks for your great help! ...

Zigster,
thanks for your great help!

genelab
Forum: Bioinformatics 09-18-2010, 12:51 AM
Replies: 5
Views: 9,211
Posted By genelab
Smile Yes, my purpose is to get the depth of read...

Yes, my purpose is to get the depth of read coverage at each nucleotide position in the contig generated by Velvet. Thanks for your great suggestion, I will try it.
Forum: Bioinformatics 09-16-2010, 06:21 AM
Replies: 5
Views: 9,211
Posted By genelab
Get coverage of each site on contig generated by Velvet

Hello everyone,
I am now working with velvet denove assemly of my short reads data. The result directory contains the following files (contigs.fa Graph2 LastGraph Log PreGraph Roadmaps ...
Forum: Bioinformatics 09-10-2010, 12:08 AM
Replies: 2
Views: 4,035
Posted By genelab
Using reference sequence in Velvet

hello all,
We have sequenced one kind of strain of a microorganism and get the pair-end short reads data. Then we want to use Velvet to assembly the genome sequence and use the genome sequence...
Forum: Bioinformatics 08-08-2010, 12:14 AM
Replies: 3
Views: 3,588
Posted By genelab
Thanks for your kindly reply. This may be the...

Thanks for your kindly reply.
This may be the default setting of "bwa aln", however, when i use 'bwa samse' to convert the result.sai ,generated by 'bwa aln', to sam format, the read in the sam...
Forum: Bioinformatics 08-07-2010, 08:59 PM
Replies: 3
Views: 3,588
Posted By genelab
How to set bwa to resport all the best repeat hit?

Hello all,
How to set bwa to resport all the best repeat hits? The default is only to report the random choosed one from all the best repeat hits.
All reply will be great appreciated. thx
Forum: Bioinformatics 08-03-2010, 09:59 PM
Replies: 4
Views: 2,277
Posted By genelab
How about the read length not equal to 75, such...

How about the read length not equal to 75, such as 50 or 100bp?

Thanks for your kindly reply
Forum: Bioinformatics 08-03-2010, 05:12 PM
Replies: 4
Views: 2,277
Posted By genelab
could anybody help me to answer this question?...

could anybody help me to answer this question? thanks!
Forum: Bioinformatics 08-01-2010, 12:36 AM
Replies: 4
Views: 2,277
Posted By genelab
Mismatch setting in BWA

Helllo everyone,

I am still comfused how to set the maximum mismatch to 2 when I use "bwa aln", given 75bp reads.

bwa aln -n 2
or
bwa -l 75 -k 2

Any suggestions will be highly...
Forum: Bioinformatics 07-30-2010, 07:11 AM
Replies: 11
Views: 21,849
Posted By genelab
This is a great suggestion, sampe with -s option...

This is a great suggestion, sampe with -s option got the same bam records as the "samtools merge" result merged from two separate end sam/bam files.

Can i ask other question, what is the reason...
Forum: Bioinformatics 07-28-2010, 06:12 PM
Replies: 11
Views: 21,849
Posted By genelab
"samtools merge" can merge the bam file,...

"samtools merge" can merge the bam file, thanks!
Forum: Bioinformatics 07-26-2010, 04:03 AM
Replies: 11
Views: 21,849
Posted By genelab
I had also used the "sampe" to get the sam result...

I had also used the "sampe" to get the sam result containing both read mapping information, however, I found many mapped read records contain softly clipped alignment, such as the sam records having...
Forum: Bioinformatics 07-25-2010, 05:43 PM
Replies: 11
Views: 21,849
Posted By genelab
I want them merged into one sam file which...

I want them merged into one sam file which contains the mapping results of both the pair-ends,
or
Should i convert the sam two bam, and then merge the two?
Forum: Bioinformatics 07-25-2010, 07:50 AM
Replies: 11
Views: 21,849
Posted By genelab
Merge sam/bam file

Hello all,
I have pair-end reads (1.fq and 2.fq ) data and mapped them with 'bwa aln', I don't want to generate alignments in the SAM format in paired-end way with 'bwa sampe', but generate sam...
Forum: Bioinformatics 07-20-2010, 06:27 AM
Replies: 1
Views: 1,409
Posted By genelab
Can maq support multiple threads?

Hi everyone,
can maq support mutiple threads (processors)? just like the "-t INT number of threads [1]" parameter in bwa or "-p/--threads <int> number of alignment threads to launch...
Forum: Bioinformatics 07-16-2010, 11:54 PM
Replies: 14
Views: 7,871
Posted By genelab
thank sowmyai for the reply!

thank sowmyai for the reply!
Forum: Bioinformatics 07-13-2010, 10:55 PM
Replies: 14
Views: 7,871
Posted By genelab
How can i set the "mismatch" parameter in bwa

Hello everyone
I want to set the number of mismatch not large than 2, when I map my short reads (75bp) to reference genome sequence with bwa, how should i set in "bwa aln".

thanks!
Forum: Bioinformatics 07-08-2010, 04:06 AM
Replies: 3
Views: 1,880
Posted By genelab
How to quick index the sam record according to the read name?

How to quick index the sam record according to the read name?

assum i hava a read which named "afaNma_1", and this read has record in the sam format file;

I want to index and get the samRecord...
Forum: Bioinformatics 07-02-2010, 11:13 PM
Replies: 2
Views: 2,742
Posted By genelab
I have found one way to figure out the problem ...

I have found one way to figure out the problem

I used the function "setValidationStringency" in samtools


thx!
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