User: Shaojiang Cai

gravatar for Shaojiang Cai
Shaojiang Cai100
Reputation:
100
Status:
Trusted
Location:
Singapore
Website:
http://www.uasis.tk
Last seen:
5 years ago
Joined:
7 years, 7 months ago
Email:
c***********@gmail.com

Ph.D student

Posts by Shaojiang Cai

<prev • 17 results • page 1 of 2 • next >
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How to define a full-length transcript for transcriptome assembly?
... Hi, I am using some RNA-seq library to test my assembler. Now what I am wondering is: HOW can we say a transcript is there? In RNA-seq libraries, can the reads be from UTR regions? If above is true, will the full UTR regions always be fully covered (or fragmented)? Usually, can I say, "transcri ...
utr rna-seq written 5.2 years ago by Shaojiang Cai100 • updated 5.2 years ago by Charles Warden7.0k
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Short Read To Short Read Aligner
... Hi, I know that BWA, Bowtie, etc can align short reads to the reference genome very efficiently. But can anybody recommend some aligner tailored to align millions of short reads to themselves? I have an application which needs to find similar reads in the library. Thanks. ...
alignment written 6.0 years ago by Shaojiang Cai100 • updated 6.0 years ago by Martin A Hansen3.0k
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Where To Download Hg19 Gene Annotation, Transcript Annotation And Cdna Fasta Files?
... Hi, I am hanging around to look for hg19 transcript annotations together with cDNA fasta files. From UCSC, I can download the gene annotation, but without transcripts. I know that I can infer from the genome once I get the transcript annotation, but is there any place where I can download the tran ...
hg19 ucsc written 6.1 years ago by Shaojiang Cai100 • updated 4.1 years ago by aebmad20
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Comment: C: Where To Find Chromosome Band?
... Thanks. I can find hg19/hg18/mm8/mm9, but would like to find spombe and ecoli. ...
written 6.2 years ago by Shaojiang Cai100
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Where To Find Chromosome Band?
... Hi, I am working on some visualization project. I would like to find the chromosome band information such as: chr1 0 2300000 p36.33 gneg chr1 2300000 5400000 p36.32 gpos25 chr1 5400000 7200000 p36.31 gneg chr1 7200000 9200000 p36.23 gpos25 chr1 920 ...
chromosome written 6.2 years ago by Shaojiang Cai100 • updated 4.8 years ago by Biostar ♦♦ 20
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Comment: C: How To Perform An Exhaustive Search (Report All Hits) Using Blat
... @istvan_albert modified. Please help ...
written 6.2 years ago by Shaojiang Cai100
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Answer: A: Is Tophat The Only Mapper To Consider For Rna-Seq Data?
... I would recommend RNA-seq blog to you. It traces all publications regarding RNA-seq. You can find most mapping tools there. ...
written 6.2 years ago by Shaojiang Cai100
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Answer: A: Finding The Best Hit From Blat Output For A Microsatellite
... I would recommend Microsoft Excel, seriously. Because best hits is your criteria, there may not be such a script tailored for you. By sorting the # of matches or # of matches / total length, you can get the hits with longest alignment lengths. Or sorting by the starting position of the reference ...
written 6.2 years ago by Shaojiang Cai100
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How To Perform An Exhaustive Search (Report All Hits) Using Blat
... I am using Blat to map long contigs to annotated transcripts. But Blat does not report all feasible hits exhaustively. For example, there is a transcript T with length 2280. If I aligned all contigs to it, Blat reports one hit with range [770, 2280]: Transcript T: ================================ ...
alignment mapping blat written 6.2 years ago by Shaojiang Cai100
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Answer: A: Error While Running Trinity Rna-Seq Assembler
... Your FASTA file may be not well formatted. You can find some validator or write a simple script to check whether some characters are not correct. For example, sequence can not contain spaces (e.g. ”akninkslsa lgnvisalae" is not valid). Anyway, it is just a text format, you can manipulate it freely ...
written 6.2 years ago by Shaojiang Cai100

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