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Search: Posts Made By: Rui Guo
Forum: Bioinformatics 11-17-2016, 05:00 PM
Replies: 0
Views: 2,330
Posted By Rui Guo
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
Posted By Rui Guo
Thank you. Can I use the flybase files? Is there...

Thank you. Can I use the flybase files? Is there a big difference between the flybase files and repeatmasker result? Also what's the difference between the flybase interspersed repeat file and...
Forum: General 07-23-2016, 12:41 AM
Replies: 2
Views: 1,504
Posted By Rui Guo
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
Posted By Rui Guo
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
Posted By Rui Guo
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
Posted By Rui Guo
Thank you. I think mapping back is redundant...

Thank you. I think mapping back is redundant because when counting it can also do that. I will try to find some other ways to do that.
Forum: Bioinformatics 05-20-2016, 08:17 PM
Replies: 4
Views: 1,143
Posted By Rui Guo
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
Posted By Rui Guo
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
Posted By Rui Guo
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
Posted By Rui Guo
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
Posted By Rui Guo
Thank you!

Thank you!
Forum: Pacific Biosciences 05-09-2016, 07:31 PM
Replies: 1
Views: 1,272
Posted By Rui Guo
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
Posted By Rui Guo
Thank you for your message!

Thank you for your message!
Forum: Pacific Biosciences 05-08-2016, 07:17 PM
Replies: 4
Views: 1,590
Posted By Rui Guo
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
Posted By Rui Guo
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
Posted By Rui Guo
Do that mean the automatically selected seeds are...

Do that mean the automatically selected seeds are long enough and has enough coverage? Does it calculate kmer frequency?
Forum: Pacific Biosciences 04-25-2016, 11:51 PM
Replies: 3
Views: 1,251
Posted By Rui Guo
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
Posted By Rui Guo
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...
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