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Search: Posts Made By: SongLi
Forum: Bioinformatics 01-23-2011, 06:29 AM
Replies: 4
Views: 3,550
Posted By SongLi
Hi Simon, Thank you for the reply. The...

Hi Simon,

Thank you for the reply.

The story is a bit compilcated.

1. I downloaded some colorspace data about a month back. Then I accidentally deleted the file, so I wanted to download...
Forum: Bioinformatics 01-22-2011, 01:03 PM
Replies: 4
Views: 3,550
Posted By SongLi
Download from SRA archive

Hi,

I recently tried to download published Colorspace results from SRA archive. http://www.ncbi.nlm.nih.gov/sra

However, I could only download sequences in ATCG. About one month back, I...
Forum: Bioinformatics 01-20-2011, 07:39 AM
Replies: 5
Views: 2,386
Posted By SongLi
Thank you for pointing out this link.

Thank you for pointing out this link.
Forum: Bioinformatics 01-19-2011, 10:02 AM
Replies: 5
Views: 2,386
Posted By SongLi
Hi, Thank you for the reply. My command is...

Hi,

Thank you for the reply. My command is included in my previous post. I did not use --trim unless it was default for colorspace alignment.

Best,
Song
Forum: Bioinformatics 01-19-2011, 09:31 AM
Replies: 5
Views: 2,386
Posted By SongLi
Bowtie colorspace output has less NT than input reads

Hi,

I am using bowtie for colorspace alignment. My data are 35nt reads (36nt if the first T is included). In the bowtie default output file, the decoded sequence space reads has only 33 NT...
Forum: Bioinformatics 12-22-2010, 07:09 AM
Replies: 3
Views: 3,436
Posted By SongLi
A little update on this issue: I wrote a...

A little update on this issue:

I wrote a script that trim off the first quality value in my fastq file. Then tophat runs smoothly through the whole analysis.

I am still not sure that's the...
Forum: Bioinformatics 12-21-2010, 11:39 AM
Replies: 3
Views: 3,436
Posted By SongLi
TopHat color space

Hi All,

I have trouble using tophat with files downloaded from SRA.

My command is:

./tophat -C -p 5 -o ./825tophat ../bowtie-0.12.7/indexes/ath_gmc_colspace_110510 ~/SRR039825.fastq

Error...
Forum: Bioinformatics 12-20-2010, 01:27 PM
Replies: 1
Views: 1,210
Posted By SongLi
Did Solid change their primer system?

Hi All,

I have a question about the reaction primers of ABI Solid sequencing.

As all you know that Solid use ligation-based sequencing. From different places on the web, two different sets of...
Forum: Bioinformatics 12-20-2010, 10:58 AM
Replies: 3
Views: 3,207
Posted By SongLi
As far as I know, quality accessment for long...

As far as I know, quality accessment for long reads has not been done. It's still an open question for now.
Forum: Bioinformatics 12-15-2010, 05:03 AM
Replies: 1
Views: 2,590
Posted By SongLi
Hi I think you need to load the .bam file...

Hi

I think you need to load the .bam file by Rsamtools, and use countOverlap after that.
Forum: Bioinformatics 11-29-2010, 11:42 AM
Replies: 23
Views: 30,008
Posted By SongLi
Hi seb567, How slow are you experiencing...

Hi seb567,

How slow are you experiencing with fasta-dump?

My experiene is this: my computer is Xeon 2.4G 4core, 12G RAM, fasta-dump takes 600 minutes to finish one sra file.

I have tried...
Forum: Bioinformatics 11-29-2010, 10:33 AM
Replies: 23
Views: 30,008
Posted By SongLi
Although I can get their CentOS 64bit running,...

Although I can get their CentOS 64bit running, it's realy slow, take about 10hrs to unpack one file. I am also interested to know more about this new SRA-tools.
Forum: Bioinformatics 11-19-2010, 11:10 AM
Replies: 0
Views: 1,336
Posted By SongLi
cufflinks with collapsed reads files

Hi Everyone,

We use cufflinks and tophat for our RNA-seq analysis. In our previous protocol, we use FASTX collapser to collapse reads with same sequence into one before doing alignments using...
Forum: Bioinformatics 11-17-2010, 04:49 AM
Replies: 7
Views: 3,709
Posted By SongLi
Thank you TopHat team for the timingly fix! ...

Thank you TopHat team for the timingly fix!

Don't know where to post, so I just post here.
Forum: Bioinformatics 11-16-2010, 01:27 PM
Replies: 7
Views: 3,709
Posted By SongLi
Hi James, Since you have solved the problem,...

Hi James,

Since you have solved the problem, would you mind post what the messages you get when the read RTF file passed?

On my side the error is:

[Tue Nov 16 17:02:17 2010] Reading known...
Forum: Bioinformatics 11-16-2010, 12:44 PM
Replies: 7
Views: 3,709
Posted By SongLi
Thank you James, However, it may not be the...

Thank you James,

However, it may not be the reason, because in the log file you posted, it says v1.1.3 there.

I still have the problem on my side.
Forum: Bioinformatics 11-16-2010, 10:19 AM
Replies: 7
Views: 3,709
Posted By SongLi
I got the same error for my dataset today,...

I got the same error for my dataset today, without those options:

tophat -o Mytophat_out -G mygtf.gtf indexes/myindex reads/myreads.fasta

The error message is :

[FAILED]
Error:...
Forum: Bioinformatics 11-16-2010, 09:14 AM
Replies: 10
Views: 10,328
Posted By SongLi
It seems that the GTF file is provided by TAIR...

It seems that the GTF file is provided by TAIR now, has anyone tried it?

ftp://ftp.arabidopsis.org/home/tair/User_Requests/TAIR9_GFF3_genes_exons.gtf

thanks,
Forum: Bioinformatics 11-11-2010, 09:26 AM
Replies: 366
Views: 193,726
Posted By SongLi
Sorry for a basic question: has anyone done a...

Sorry for a basic question: has anyone done a benchmark to see how these quality scores affect the final output?

Thanks
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