Forum: Bioinformatics
11-17-2016, 05:00 PM
|
|
Replies: 0
Views: 2,330
sam file total matched base and total bases
I have a fasta, most of the sequence is from repeat region, so they can be mapped to reference in sam lots of times. I use bwa mem with "-a" option, so they appear many times in different position of...
|
|
Forum: General
07-23-2016, 07:34 PM
|
|
Replies: 2
Views: 1,504
|
|
Forum: General
07-23-2016, 12:41 AM
|
|
Replies: 2
Views: 1,504
repbase and flybase
I want to make a gff file about the TE in fly, so I can see the repeat position in IGV. I can use repeatmasker, based on the repeat data from repbase file drorep.ref, which contains 238 sequences. I...
|
|
Forum: Bioinformatics
05-28-2016, 12:27 AM
|
|
Replies: 0
Views: 951
wgs assembler
What does the -partition parameter mean in wgs-8.3 assembler? If I partition the reads, can I find all the overlaps?
|
|
Forum: Pacific Biosciences
05-25-2016, 01:30 AM
|
|
Replies: 0
Views: 1,020
MHAP pipeline
I'm using canu, and I want to know if it's possible to just use MHAP to find alignment and use PBDAGCON or falcon_sense just to generate consensus sequences, then not to assembly the consensus...
|
|
Forum: Bioinformatics
05-25-2016, 12:31 AM
|
|
Replies: 4
Views: 1,143
|
|
Forum: Bioinformatics
05-20-2016, 08:17 PM
|
|
Replies: 4
Views: 1,143
kmer counting software issue
There are many kmer counting software. If just to find repeats, can I just use someone that can count frequency and can give the kmer position in the genome(or reads), and then align the high...
|
|
Forum: Pacific Biosciences
05-18-2016, 07:42 PM
|
|
Replies: 1
Views: 2,834
pacbio reads alignment
Which software is proper for pacbio reads alignment to reference genome? I see bwa mem is ok, and there is blasr, but slow. How about MHAP? But from the manual it says the output is blasr m4 format,...
|
|
Forum: Illumina/Solexa
05-15-2016, 07:38 PM
|
|
Replies: 0
Views: 1,096
1000genome read download
I want to download a 10x below raw read of NA12889. I see that in ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12889/sequence_read
There are many files, how to choose between those files?
|
|
Forum: Pacific Biosciences
05-13-2016, 01:45 AM
|
|
Replies: 1
Views: 1,072
mhap polished sequence
What is mhap polished sequences in the page http://www.cbcb.umd.edu/software/PBcR/MHAP/
Are those corrected reads, but not assembled?
|
|
Forum: Pacific Biosciences
05-13-2016, 01:40 AM
|
|
Replies: 4
Views: 1,590
|
|
Forum: Pacific Biosciences
05-09-2016, 07:31 PM
|
|
Replies: 1
Views: 1,272
pbsim vs readsim
I want to simulate pacbio reads from real reads and assembly. I hope it can simulate the error and length distribution or and simulate perfect reads and length distribution. I see there are two...
|
|
Forum: Pacific Biosciences
05-09-2016, 07:06 PM
|
|
Replies: 4
Views: 1,590
|
|
Forum: Pacific Biosciences
05-08-2016, 07:17 PM
|
|
Replies: 4
Views: 1,590
PacbioToCA and PBcR
I read the paper Reducing assembly complexity of microbial genomes with single-molecule sequencing, and I find it use PacbioToCA to do self-correction. But I think PacbioToCA uses short reads(NGS...
|
|
Forum: Bioinformatics
05-05-2016, 11:49 PM
|
|
Replies: 1
Views: 921
teclass paper
I want to do something like TEclass for my homework:) I don't understand what "tetramer" and "pentamer" mean in their paper. That method builds tow complete sets of classifiers using tetramers and...
|
|
Forum: Pacific Biosciences
04-26-2016, 03:50 PM
|
|
Replies: 3
Views: 1,251
|
|
Forum: Pacific Biosciences
04-25-2016, 11:51 PM
|
|
Replies: 3
Views: 1,251
hgap seed seletion step
I want to know how hgap select the seed. The paper says it selects the seed with more than 20x coverage, but doesn't say how it counts the coverage.
|
|
Forum: Pacific Biosciences
04-19-2016, 07:35 PM
|
|
Replies: 2
Views: 1,406
Can I use velvet to assemble SMRT reads?
I don't know whether it's possible to use velvet to assemble SMRT reads. Also I want to know how to know the read coverage of SMRT. Is that a function of the number of the SMRT cells? What other...
|
