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Forum: Bioinformatics 12-29-2010, 01:58 PM
Replies: 4
Views: 1,940
Posted By HTS
Yes, I am having the same problem after upgrading...

Yes, I am having the same problem after upgrading to "samtools-0.1.12a". I guess it should be an easy fix, just hope the TopHat guys can find time to do it soon (or if the samtools guys can stick to...
Forum: Bioinformatics 10-05-2010, 06:09 AM
Replies: 13
Views: 3,358
Posted By HTS
I am running Ubuntu 10.04 LTS 64-bit

I am running Ubuntu 10.04 LTS 64-bit
Forum: Bioinformatics 10-04-2010, 08:08 PM
Replies: 13
Views: 3,358
Posted By HTS
Exclamation More errors with TopHat 1.1.0

Thanks Daehwan for quickly fixing the previous error of TopHat 1.1.0 on SE reads! As I am trying the updated version, I got stuck again at prep_reads with standard 75nt Illumina SE reads. The same...
Forum: Bioinformatics 10-04-2010, 06:23 PM
Replies: 4
Views: 2,179
Posted By HTS
Question Does TopHat support Unix piping?

Hi,

I know Bowtie supports piping (although not so convenient to use for paired-end reads), and I am wondering if TopHat does the same. I tried something like "gzip -dc $fq | tophat $genome -"...
Forum: Illumina/Solexa 12-19-2009, 08:18 AM
Replies: 0
Views: 2,759
Posted By HTS
Sequencing bias on the Illumina platform

Hi,

I am trying to take a close look at the sequencing bias present in the Illumina platform and to think about ways to correct for it algorithmically, especially in the context of RNA-Seq. My...
Forum: Bioinformatics 12-14-2009, 01:32 PM
Replies: 8
Views: 7,198
Posted By HTS
Thanks for your reply, Brandon! I guess I didn't...

Thanks for your reply, Brandon! I guess I didn't make myself clear but I need something considerably more sophisticated than concatenating multiple text files, especially considering what each field...
Forum: Bioinformatics 12-14-2009, 01:08 PM
Replies: 8
Views: 7,198
Posted By HTS
Hi Cole, I am aware of the bed_to_juncs...

Hi Cole,

I am aware of the bed_to_juncs script but when converting BED files to .junc files, it doesn't preserve the score and overhang information that I would like to combine. BTW, could you...
Forum: Bioinformatics 12-14-2009, 12:23 PM
Replies: 10
Views: 1,731
Posted By HTS
It seems that it didn't even pass the read...

It seems that it didn't even pass the read checking stage. Did you see an error message in prep_reads.log?
Forum: Bioinformatics 12-14-2009, 12:11 PM
Replies: 8
Views: 7,198
Posted By HTS
How to combine junctions.bed files produced by TopHat

Hi,

Basically I would like to double check before writing my own script to do so. Since I need to pool together samples with different read lengths, I have to run TopHat separately for them...
Forum: Introductions 12-07-2009, 07:07 PM
Replies: 3
Views: 1,812
Posted By HTS
Thanks for your reply! I moved to Toronto 4...

Thanks for your reply! I moved to Toronto 4 years ago. I am a researcher.
Forum: Bioinformatics 12-07-2009, 08:05 AM
Replies: 6
Views: 9,182
Posted By HTS
Please allow me to ask two related questions: ...

Please allow me to ask two related questions:

1. If I do use TopHat and Bowtie to do the alignment, will the mapping qualities of multireads be automatically adjusted? From the Bowtie manual it...
Forum: Bioinformatics 11-25-2009, 12:59 PM
Replies: 3
Views: 2,002
Posted By HTS
Yes, I got the same error and have reported the...

Yes, I got the same error and have reported the bug to Cole Trapnell. Try to look for the line says "chrM 0 0 0" and delete it, and it should solve the problem (at least it works in my case).

--...
Forum: Bioinformatics 11-24-2009, 08:24 PM
Replies: 14
Views: 4,408
Posted By HTS
When I read through this post, I become really...

When I read through this post, I become really confused:

1. It is obvious from the original post that Bowtie reports 0-based alignments while MAQ reports 1-based ones, not the other way around.
...
Forum: Bioinformatics 11-23-2009, 01:42 PM
Replies: 16
Views: 17,804
Posted By HTS
I see. Thanks for the explanation! The reason...

I see. Thanks for the explanation! The reason gtf2gff3 doesn't work for you is probably because you forgot to convert chromosome names in the Ensembl convention to the UCSC convention? I forgot...
Forum: Bioinformatics 11-23-2009, 01:16 PM
Replies: 16
Views: 17,804
Posted By HTS
Thanks a lot for the coding effort and for...

Thanks a lot for the coding effort and for sharing your script! But are you aware of this one <http://song.cvs.sourceforge.net/viewvc/song/software/scripts/gtf2gff3/>, which has been out there for...
Forum: Bioinformatics 11-21-2009, 07:25 PM
Replies: 8
Views: 2,700
Posted By HTS
Thanks for your clarification, Heng! I checked...

Thanks for your clarification, Heng! I checked hg19 and NCBI 37.1 the other day and they are exactly the same, i.e., both don't include chrN_random now. Personally I stick with UCSC for convenience...
Forum: Bioinformatics 11-21-2009, 08:35 AM
Replies: 8
Views: 2,700
Posted By HTS
You are welcome! I simply used top to take a...

You are welcome! I simply used top to take a rough look at the memory used by bowtie-build, but you could use more sophisticated tools such as memtime or tstime if you want. If memory is really an...
Forum: Bioinformatics 11-21-2009, 07:08 AM
Replies: 8
Views: 2,700
Posted By HTS
64-bit Linux shouldn't have the 2GB file limit,...

64-bit Linux shouldn't have the 2GB file limit, so I am not sure what causes your problem, but pre-built indexes of hg18 and hg19 (with headers chr1, chr2 etc) can be readily downloaded from the...
Forum: Bioinformatics 11-20-2009, 06:55 PM
Replies: 1
Views: 1,813
Posted By HTS
Further breaking down reads as short as 32 or...

Further breaking down reads as short as 32 or 36bp doesn't seem to be a sensible thing to me. I wouldn't use segments shorter than 25bp myself. Doesn't the default setting more or less work for you...
Forum: Bioinformatics 11-20-2009, 02:23 PM
Replies: 16
Views: 11,847
Posted By HTS
Great, thanks a lot! I can't wait to try things...

Great, thanks a lot! I can't wait to try things out:)!
Forum: Bioinformatics 11-20-2009, 02:12 PM
Replies: 16
Views: 11,847
Posted By HTS
Thanks a lot for your quick reply, Nils! Could...

Thanks a lot for your quick reply, Nils! Could you give me a bit more details about how to do this? I remember in your paper you said when the best alignment of a read map to more than one...
Forum: Bioinformatics 11-20-2009, 01:28 PM
Replies: 16
Views: 11,847
Posted By HTS
Performing true local alignment with BFAST?

Hi Nils,

It is nice to read your paper, and I hope that my question is not completely out of the context (admittedly I haven't got time to dig into the details of your implementation yet). ...
Forum: Introductions 11-20-2009, 12:02 PM
Replies: 3
Views: 1,812
Posted By HTS
Cool Hello from Toronto (大家好)

Hi,

I have been analyzing Illumina HTS data, mostly RNA-Seq, for a while now at the University of Toronto, but only discovered this forum quite recently:o. I am interested in the data analysis...
Forum: RNA Sequencing 11-20-2009, 11:37 AM
Replies: 2
Views: 2,164
Posted By HTS
Alternatively, you could download hg18/19 indexes...

Alternatively, you could download hg18/19 indexes from the Bowtie website and use them from now on (what you see now is a result of using the indexes built by NCBI assemblies), which use chromosome...
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