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Search: Posts Made By: lmf_bill
Forum: Bioinformatics 11-14-2011, 01:17 PM
Replies: 4
Views: 4,127
Posted By lmf_bill
I got the similar problems. For some genes...

I got the similar problems. For some genes without isoforms, cufflinks or cuffdiff estimate 0 FPKM, but the real case is they are expressed high.
Forum: RNA Sequencing 10-25-2011, 06:42 AM
Replies: 5
Views: 6,780
Posted By lmf_bill
As ngsbee mentioned: you must make...

As ngsbee mentioned:

you must make consistence of chromosome name. Sometime, 1, 2,3,...22,X,Y, M used as chromosome name, but sometime chr1, chr2,chr3,...chrM were used as chromosome name. You...
Forum: Introductions 04-15-2011, 06:53 PM
Replies: 4
Views: 1,634
Posted By lmf_bill
http://en.wikipedia.org/wiki/Phred_quality_score,...

http://en.wikipedia.org/wiki/Phred_quality_score,
maybe, you can get the answer.
Forum: Bioinformatics 03-06-2011, 10:45 AM
Replies: 3
Views: 2,190
Posted By lmf_bill
it is normal. Some annotation differences are...

it is normal. Some annotation differences are between different annotation database.
Forum: Bioinformatics 11-20-2010, 04:25 AM
Replies: 11
Views: 2,197
Posted By lmf_bill
correctly, it is hard to estimate the expression...

correctly, it is hard to estimate the expression of overlapping genes by RNASeq within popular protocol. It will be possible for the short part overlapping genes.
Forum: RNA Sequencing 11-03-2010, 01:13 PM
Replies: 15
Views: 18,194
Posted By lmf_bill
you should be careful of these genes. In my...

you should be careful of these genes. In my points, you do not need calculate the fold change. You can split these cases into two situations: one condition is larger or smaller than threshold, e.g....
Forum: Events / Conferences 09-27-2010, 11:07 AM
Replies: 9
Views: 7,785
Posted By lmf_bill
Is it still available? I am interested it.

Is it still available? I am interested it.
Forum: Bioinformatics 07-30-2010, 05:43 AM
Replies: 5
Views: 6,843
Posted By lmf_bill
yes, If you only want to get the location...

yes, If you only want to get the location transfer, liftover is faster. In the mean time, many novel cases need to be consider, just as you said you can get more info from the newer assembly....
Forum: Bioinformatics 07-29-2010, 12:53 PM
Replies: 5
Views: 6,843
Posted By lmf_bill
I think the best way is to remap against hg19. It...

I think the best way is to remap against hg19. It will take the similar time when you use liftover to transfer hg18 to hg19. Good lucky!
Forum: Bioinformatics 06-21-2010, 07:09 AM
Replies: 11
Views: 12,141
Posted By lmf_bill
Using tophat, especial for paired-end reads, it...

Using tophat, especial for paired-end reads, it will take long time. In my personal point, your configuration is enough.
BTW, tophat will produce huge tmp file.
Forum: General 06-18-2010, 02:19 AM
Replies: 2
Views: 13,575
Posted By lmf_bill
yes, UTR, especial 3UTR has different feature...

yes, UTR, especial 3UTR has different feature from other exons. I think it depends on your focus.
Forum: De novo discovery 06-18-2010, 02:12 AM
Replies: 4
Views: 3,383
Posted By lmf_bill
I remember abyss suggests using k value loop to...

I remember abyss suggests using k value loop to find the proper one.
Forum: Bioinformatics 06-14-2010, 05:12 AM
Replies: 8
Views: 14,230
Posted By lmf_bill
"export PATH only change the current session....

"export PATH only change the current session. Once you log out, anything you've added to the path will be removed. "

If you do not log out, I guess tophat does not accept this way of PATH setting....
Forum: Bioinformatics 06-09-2010, 10:14 AM
Replies: 6
Views: 4,164
Posted By lmf_bill
Try the sequence read archive (SRA) in NCBI entry

Try the sequence read archive (SRA) in NCBI entry
Forum: Illumina/Solexa 06-08-2010, 01:25 PM
Replies: 5
Views: 2,379
Posted By lmf_bill
I guess sequence file is consistent with...

I guess sequence file is consistent with *.sorted.txt file
Forum: Illumina/Solexa 06-08-2010, 01:22 PM
Replies: 1
Views: 1,443
Posted By lmf_bill
it seems to be some novel segments.

it seems to be some novel segments.
Forum: Bioinformatics 06-08-2010, 01:11 PM
Replies: 8
Views: 14,230
Posted By lmf_bill
just do as zorph said. I think you need learn...

just do as zorph said. I think you need learn something about Linux/Unix/Mac.
.bashrc or .bash_profile locate in your home folder.
In the terminal, you can use "cd ~" to enter. then use "ls -a"...
Forum: Literature Watch 04-09-2010, 12:16 PM
Replies: 1
Views: 2,896
Posted By lmf_bill
great work, personal genome sequencing is coming.

great work, personal genome sequencing is coming.
Forum: RNA Sequencing 04-09-2010, 12:11 PM
Replies: 5
Views: 3,409
Posted By lmf_bill
I think for tophat, it does not report fusion...

I think for tophat, it does not report fusion transcript from different chromosome
Forum: RNA Sequencing 04-09-2010, 12:06 PM
Replies: 2
Views: 3,240
Posted By lmf_bill
It is one general status for RNA-seq data. I...

It is one general status for RNA-seq data. I agree with Jon_Keats explanation "poly-A mRNA selection bias"
Forum: Illumina/Solexa 02-25-2010, 06:29 AM
Replies: 2
Views: 3,086
Posted By lmf_bill
nod what about the 5 primer error rate, it...

nod
what about the 5 primer error rate, it seems due to primer.
Forum: RNA Sequencing 01-24-2010, 09:14 PM
Replies: 14
Views: 6,885
Posted By lmf_bill
RE: 1. for more information of gff3, you can...

RE:
1. for more information of gff3, you can search by google. It is complex to get gff3 for human genome. First, you get gtf from ensembl, then convert them to gff3 by some perl script...
Forum: RNA Sequencing 01-20-2010, 03:54 PM
Replies: 11
Views: 13,999
Posted By lmf_bill
in biomart:http://www.biomart.org/ first...

in biomart:http://www.biomart.org/
first martview-->choose database(ensembl56 sanger UK)--> GRCH37-->fiters-->gene-->gene type-->rRNA
you can get more information from this websit
Forum: RNA Sequencing 01-20-2010, 12:09 AM
Replies: 2
Views: 4,284
Posted By lmf_bill
I think your question is relative to multiple...

I think your question is relative to multiple hits of one read. It one hard work. Some recent papers published in Bioinformatics have put forward some approaches to resolve this problem, you can...
Forum: RNA Sequencing 01-19-2010, 11:58 PM
Replies: 11
Views: 13,999
Posted By lmf_bill
if my correct understanding, you want to get the...

if my correct understanding, you want to get the list of rRNA in Human. if so, you can get it by using biomart.
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