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Search: Posts Made By: xinwu
Forum: Bioinformatics 01-03-2012, 09:40 PM
Replies: 5
Views: 5,224
Posted By xinwu
It seems that bowtie does not guarantee to find...

It seems that bowtie does not guarantee to find the best match, after several tries, it may give up.
Forum: Bioinformatics 02-22-2011, 06:34 PM
Replies: 3
Views: 2,082
Posted By xinwu
I have another feature request about bowtie...

I have another feature request about bowtie trimming option both from 3 end and 5 end. So far, we have to trim the low quality bases manually and it take redundant space for trimmed read files.
Forum: Bioinformatics 12-27-2010, 01:08 AM
Replies: 3
Views: 3,374
Posted By xinwu
This is due to the format used by NCBI. NCBI...

This is due to the format used by NCBI. NCBI transforms all the data from different platforms to a standard FASTQ format.
Tophat uses bowtie for reads mapping and it expects csfasta and qual files...
Forum: Bioinformatics 12-22-2010, 10:33 PM
Replies: 0
Views: 2,195
Posted By xinwu
samtools flagstats bug or it does not support multi-reads?

Hi All,
I used bowtie to map reads with k = 10 (allow at most 10 alignments for one read). I hoped to get some statistical result for mapping but found the summary of bowtie result was not...
Forum: Bioinformatics 12-21-2010, 01:19 AM
Replies: 3
Views: 3,143
Posted By xinwu
As manual said "read length can be 1024". Do you...

As manual said "read length can be 1024". Do you mean seq quality will be ignored when it is a long read? If so, what's the max length? Only n mode considering seq quality, will it affect v mode?
Forum: Bioinformatics 12-21-2010, 01:16 AM
Replies: 3
Views: 3,143
Posted By xinwu
IMO, if you want to allow more number of...

IMO, if you want to allow more number of mismatches, you can only use n mode with large e value, since both n or v option only allow at most 3 mismatches. Say, you can set -n 3 with larger e value.
Forum: Bioinformatics 12-16-2010, 10:08 PM
Replies: 11
Views: 3,855
Posted By xinwu
As the manual said "A stronger form of uniqueness...

As the manual said "A stronger form of uniqueness is enforced when -m is specified but --best and --strata are not.", your conclusion is right. It is interesting when you play with "strata". In your...
Forum: Bioinformatics 12-16-2010, 01:40 AM
Replies: 11
Views: 3,855
Posted By xinwu
As you said, you want 'unique' alignment rather...

As you said, you want 'unique' alignment rather than all aliginment, just use m with 1 to achieve this goal.
Forum: Bioinformatics 12-16-2010, 01:38 AM
Replies: 11
Views: 3,855
Posted By xinwu
fkrueger is right. Other options make no sense...

fkrueger is right. Other options make no sense since you set m option with 1.
Forum: Bioinformatics 12-16-2010, 01:26 AM
Replies: 11
Views: 3,855
Posted By xinwu
IMO, all option only means all valid alignments...

IMO, all option only means all valid alignments ACCORDING TO YOUR CRITERIA. Since you set m option with 1, all option does nothing here. If you set m with 3, and without all option, reads with 2...
Forum: Bioinformatics 12-16-2010, 01:22 AM
Replies: 4
Views: 2,699
Posted By xinwu
You have the answer and should consider the...

You have the answer and should consider the strand.
Forum: Bioinformatics 12-16-2010, 01:19 AM
Replies: 17
Views: 6,452
Posted By xinwu
What's your segment size?

What's your segment size?
Forum: Bioinformatics 12-14-2010, 08:09 PM
Replies: 8
Views: 2,076
Posted By xinwu
I've checked all read names, the max length of...

I've checked all read names, the max length of them is 37. I've tried a small set with 1000 reads, it worked fine. The original reads file is about 7G with ~130M reads (100bp). Does its size matter?
Forum: Bioinformatics 12-13-2010, 10:57 PM
Replies: 1
Views: 1,386
Posted By xinwu
What's the acceptable solution to improve sensibility for short reads mapping

Hi All,
I am here to look for acceptable solutions for my goals of short reads mapping.
Goal 1: mapping short reads as fast as possible
Goal 2: if number of mapped reads is low, improve it
Goal...
Forum: Bioinformatics 12-13-2010, 10:16 PM
Replies: 8
Views: 2,076
Posted By xinwu
Thanks for the quick reply, Nils. But I am sure...

Thanks for the quick reply, Nils. But I am sure the name should not exceed
4028 which is really a large number for a name. There must be something wrong somewhere.
Forum: Bioinformatics 12-13-2010, 07:15 PM
Replies: 8
Views: 2,076
Posted By xinwu
I met the same issue. After rerun it, It still...

I met the same issue. After rerun it, It still threw this exception. I tested the data with Bowtie, it worked. So, what is the read name check? and why it failed in this step? Thanks.
Forum: Bioinformatics 12-07-2010, 05:57 PM
Replies: 0
Views: 1,392
Posted By xinwu
Strange behavior of BWA

Hi All,
I have ~100M Illumina RNA-Seq file in fastq format. After I ran BWA algn against trascriptome(all available cDNAs in fasta format, indexed by BWA), I got ~300M sai file. Then I ran BWA samse...
Forum: Bioinformatics 12-07-2010, 05:37 PM
Replies: 14
Views: 6,657
Posted By xinwu
Thanks for all of you. Does Bowtie output...

Thanks for all of you. Does Bowtie output alignment score somewhere? If Bowtie has alignment score for each alignment, I would like to see it rather than use --best --strata combination. In other...
Forum: Bioinformatics 12-07-2010, 12:44 AM
Replies: 14
Views: 6,657
Posted By xinwu
What does strata mean in Bowtie?

Hi All,
Although I've read the manual of Bowtie, I can not quite understand the report option of 'strata' mean. I know -a will output all the alignments and --best will report alignments in...
Forum: Bioinformatics 12-06-2010, 12:22 AM
Replies: 78
Views: 26,738
Posted By xinwu
I run into the same error with you when I use...

I run into the same error with you when I use another genome. No ideas... :(
Another BWA run at background over 70 hours when generate SAM file from SAI file for transcriptome.
Forum: Bioinformatics 11-30-2010, 06:44 PM
Replies: 9
Views: 19,198
Posted By xinwu
Ben, So, does Bowtie give its own mapping...

Ben,
So, does Bowtie give its own mapping quality values somewhere or it does not report any mapping quality values at all? As the manual said, --best option can report best-worst order alignments,...
Forum: Bioinformatics 09-09-2010, 11:00 PM
Replies: 5
Views: 2,723
Posted By xinwu
Hi Ben, One more question :), Bowtie is based...

Hi Ben,
One more question :), Bowtie is based on BWT and Cloudburst is based on seed-extended like RMAP. Is it true that seed-extended is higher sensitive and fewer limitation (say, allow gap and...
Forum: Bioinformatics 09-09-2010, 01:25 AM
Replies: 4
Views: 5,086
Posted By xinwu
BAM, Zlib and BGZF library

Hi all,
There is few information in SAMTools website and the published paper about BAM. In the paper, the author said BAM is based on the Zlib and used BGZF library. I just wonder where can I find...
Forum: Bioinformatics 09-03-2010, 01:49 AM
Replies: 9
Views: 13,403
Posted By xinwu
SAMTool install error about curses

Hi all,
When I install SAMTool 0.1.8 on linux, I got error: cannot find -lcurses
collect2: ld returned 1 exit status
But I have libncurses.so installed under /usr/lib.
After run rpm -qa | grep...
Forum: Bioinformatics 09-02-2010, 06:11 PM
Replies: 3
Views: 3,322
Posted By xinwu
Hi Krobison, Thanks a lot. We're planning to...

Hi Krobison,
Thanks a lot. We're planning to make a shorts reads assembly software review and comparison and look for a de facto standard data set as our benchmark. Although human genome is a well...
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