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Forum: Bioinformatics 05-10-2011, 11:32 PM
Replies: 0
Views: 1,728
Posted By baohua100
allele-specific expression

For ASE test, we do binomial test for each heterozygous SNP to see wheather it's ASE.

But Some transcripts will have more than one heterozygous SNP. However we tests each SNP independently. Is...
Forum: Bioinformatics 05-01-2011, 01:02 AM
Replies: 0
Views: 1,678
Posted By baohua100
allele-specific expression by direct genome and transcritpome sequencing

We sequenced the diploid genome of a single individual and their transcritome.
(Poplar)

Fisrt, we identiy all the heterozygosity SNPs (genome).

If i know it's a heterozygosity SNPs, Should I...
Forum: RNA Sequencing 05-01-2011, 12:59 AM
Replies: 1
Views: 2,468
Posted By baohua100
Smile Test of allele-specific expression by genome and transcritome sequencing

We sequenced the diploid genome of a single individual and their transcritome.
(Poplar)

Fisrt, we identiy all the heterozygosity SNPs (genome).

If i know it's a heterozygosity SNPs, Should I...
Forum: Bioinformatics 11-27-2009, 07:52 PM
Replies: 0
Views: 1,544
Posted By baohua100
linkage disequilibrium

we have sequenced (solexa) 20 individuals genomes and called SNPs

can we know the linkage disequilibrium on the genome-scale?
Forum: Bioinformatics 09-29-2009, 12:05 PM
Replies: 4
Views: 1,791
Posted By baohua100
Mapping to the genome and to see how many reads...

Mapping to the genome and to see how many reads mapped to the exons, introns and intergenic region.

You can then use reads that mapped to the intergenic region to identify novel transcript.
Forum: Bioinformatics 09-23-2009, 10:09 AM
Replies: 0
Views: 1,209
Posted By baohua100
Intron retain detection using Solexa RNA-seq

We first find all possible junction alignment and then search all junctions. If all the sites between two junction site are covered by reads, then we identify a intron retain.

Is this OK? There...
Forum: RNA Sequencing 09-23-2009, 09:47 AM
Replies: 0
Views: 1,853
Posted By baohua100
Intron retain detection using Solexa RNA-seq

We first find all possible junction alignment and then search all junctions. If all the sites between two junction site are covered by reads, then we identify a intron retain.

Is this OK? There...
Forum: Bioinformatics 08-26-2009, 08:23 PM
Replies: 6
Views: 2,927
Posted By baohua100
-M <int> match mode for each read or the seed...

-M <int> match mode for each read or the seed part of read, which shouldn't contain more than 2 mismaches, [4]
0: exact match only
1: 1 mismatch match only
2: 2 mismatch match only
4: find the...
Forum: Bioinformatics 08-26-2009, 06:00 PM
Replies: 6
Views: 2,927
Posted By baohua100
SOAP2 -v doesn't work

SOAP2 -v maximum number of mismatches allowed on a read

I have tried -v 3 -v 2 -v 4 for 50bp read, but the maximum number of mismatch in the output is always 2. there are no read wish mismatch 3...
Forum: Bioinformatics 08-23-2009, 10:30 AM
Replies: 0
Views: 1,171
Posted By baohua100
RNA-seq reads BLAT

After align the reads to genome and junction sequences, I align the lefted reads to genome using BLAT. The read length: some 36bp and some 50bp.

BLAT outputs the PSL files. How can I use this...
Forum: Bioinformatics 08-23-2009, 10:02 AM
Replies: 4
Views: 5,509
Posted By baohua100
yes, it's ok now

yes, it's ok now
Forum: Bioinformatics 08-22-2009, 08:12 PM
Replies: 2
Views: 2,914
Posted By baohua100
RPKM for alternative splicing genes?

When calculate a PRKM for a gene locus

R=109C/NL
where C is the number of mappable reads that fell onto the gene’s exons, N is the total number of mappable reads in the experiment, and L is the...
Forum: RNA Sequencing 08-22-2009, 08:05 PM
Replies: 9
Views: 11,776
Posted By baohua100
no one show how to use paired-end info to infer...

no one show how to use paired-end info to infer junction and alternative splicing?
Forum: Bioinformatics 08-22-2009, 07:36 PM
Replies: 4
Views: 5,509
Posted By baohua100
It's mode is 775 . -rw-rw-r-- 1 populus...

It's mode is 775 .

-rw-rw-r-- 1 populus populus 120240 2003-09-18 21:23 11.ooc
-rwxrwxr-x 1 populus populus 225708 2007-04-20 19:59 blat
-rw-r--r-- 1 populus populus 829907 2007-04-20 19:58...
Forum: Bioinformatics 08-22-2009, 12:53 AM
Replies: 4
Views: 5,509
Posted By baohua100
BLAT problem

i have download BLAT form
http://genome-test.cse.ucsc.edu/~kent/exe/linux/blatSuite.34.zip

the computer : 64bit Ubuntu

after unzip the file, when i use ./blat

-bash: ./blat: No...
Forum: Bioinformatics 08-20-2009, 09:05 PM
Replies: 4
Views: 12,526
Posted By baohua100
How can I pileup all the sites of reference...

How can I pileup all the sites of reference sequence , but not only the sites covered by at least 1 ?
Forum: Bioinformatics 08-20-2009, 01:10 PM
Replies: 0
Views: 3,387
Posted By baohua100
samtool sam to bam error!

/home/populus/samtools-0.1.5c_x86_64-linux/samtools import ../../../baohua/junction_seq/junction.fasta junction.sam junction.bam


[sam_read1] reference '430624:LG_XIII:729449:k:-:726374:727070'...
Forum: Bioinformatics 08-19-2009, 10:30 PM
Replies: 19
Views: 19,374
Posted By baohua100
samtools faidx Segmentation fault

populus@Rust:~/samtools-0.1.5c_x86_64-linux$ ./samtools faidx /media/Poplar/baohua/genome/poplar_genome.fa
[fai_build_core] different line length in sequence 'scaffold_28'.
Segmentation fault
...
Forum: Bioinformatics 08-19-2009, 09:59 PM
Replies: 6
Views: 9,523
Posted By baohua100
mapping quality score 10, what's the error...

mapping quality score 10, what's the error probability?
Forum: Bioinformatics 08-19-2009, 12:28 PM
Replies: 0
Views: 1,274
Posted By baohua100
MAQ paired-end alignment parameters

maq map aln.map ref.bfa 1.bfq 2.bfq -a 500

-a INT max distance between two paired reads [250]

when I use -a 500 the alignmnet output also contains the pairs whose distance is larger than...
Forum: Bioinformatics 08-19-2009, 12:22 PM
Replies: 3
Views: 2,420
Posted By baohua100
MAQ's mapview format to binary map format

maq map aln.map ref.bfa reads.bfq

maq mapview aln.map > aln.out

The aln.out is text file and aln.map is binary file.

I filter some reads in aln.out and want to convert the new aln.out to...
Forum: Bioinformatics 08-16-2009, 10:45 AM
Replies: 1
Views: 1,777
Posted By baohua100
Local UCSC genome browser server

We have some wig files (solexa mapping results).

The reference genome is Poplar (Populus). The UCSC does not provide this genome. We have genome sequence and GFF file.

Can we set up a local...
Forum: Bioinformatics 08-14-2009, 01:53 PM
Replies: 30
Views: 18,448
Posted By baohua100
How about paired-end reads? When I use...

How about paired-end reads?

When I use fq_all2std.pl , it only output single-end
Forum: Bioinformatics 08-12-2009, 07:48 PM
Replies: 15
Views: 4,535
Posted By baohua100
the file produced by using the '-H' option , ...

the file produced by using the '-H' option ,

This file contains multiple hit reads? or ?
Forum: Bioinformatics 08-12-2009, 06:52 PM
Replies: 15
Views: 4,535
Posted By baohua100
So maq can not tell anything about unique hit or...

So maq can not tell anything about unique hit or multiple hit ?

Just a mapping quality score ?


How we choose use which mapping results, for later analysis
Showing results 1 to 25 of 103

 


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