Forum: Bioinformatics
05-11-2011, 12:32 AM
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Replies: 0
Views: 1,958
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...
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Forum: Bioinformatics
05-01-2011, 02:02 AM
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Replies: 0
Views: 1,859
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Forum: RNA Sequencing
05-01-2011, 01:59 AM
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Replies: 1
Views: 2,682
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Forum: Bioinformatics
11-27-2009, 08:52 PM
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Replies: 0
Views: 1,706
linkage disequilibrium
we have sequenced (solexa) 20 individuals genomes and called SNPs
can we know the linkage disequilibrium on the genome-scale?
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Forum: Bioinformatics
09-29-2009, 01:05 PM
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Replies: 4
Views: 1,960
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Forum: Bioinformatics
09-23-2009, 11:09 AM
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Replies: 0
Views: 1,373
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...
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Forum: RNA Sequencing
09-23-2009, 10:47 AM
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Replies: 0
Views: 2,196
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...
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Forum: Bioinformatics
08-26-2009, 09:23 PM
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Replies: 6
Views: 3,212
-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...
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Forum: Bioinformatics
08-26-2009, 07:00 PM
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Replies: 6
Views: 3,212
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...
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Forum: Bioinformatics
08-23-2009, 11:30 AM
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Replies: 0
Views: 1,281
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...
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Forum: Bioinformatics
08-23-2009, 11:02 AM
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Replies: 4
Views: 5,785
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Forum: Bioinformatics
08-22-2009, 09:12 PM
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Replies: 2
Views: 3,141
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...
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Forum: RNA Sequencing
08-22-2009, 09:05 PM
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Replies: 9
Views: 12,321
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Forum: Bioinformatics
08-22-2009, 08:36 PM
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Replies: 4
Views: 5,785
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...
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Forum: Bioinformatics
08-22-2009, 01:53 AM
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Replies: 4
Views: 5,785
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...
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Forum: Bioinformatics
08-20-2009, 10:05 PM
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Replies: 4
Views: 13,214
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Forum: Bioinformatics
08-20-2009, 02:10 PM
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Replies: 0
Views: 3,570
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'...
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Forum: Bioinformatics
08-19-2009, 11:30 PM
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Replies: 19
Views: 20,861
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
...
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Forum: Bioinformatics
08-19-2009, 10:59 PM
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Replies: 6
Views: 10,116
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Forum: Bioinformatics
08-19-2009, 01:28 PM
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Replies: 0
Views: 1,424
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...
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Forum: Bioinformatics
08-19-2009, 01:22 PM
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Replies: 3
Views: 2,644
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...
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Forum: Bioinformatics
08-16-2009, 11:45 AM
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Replies: 1
Views: 1,987
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...
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Forum: Bioinformatics
08-14-2009, 02:53 PM
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Replies: 30
Views: 19,598
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Forum: Bioinformatics
08-12-2009, 08:48 PM
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Replies: 15
Views: 4,911
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Forum: Bioinformatics
08-12-2009, 07:52 PM
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Replies: 15
Views: 4,911
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