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Search: Posts Made By: chenyao
Forum: Bioinformatics 09-04-2011, 05:57 AM
Replies: 5
Views: 4,628
Posted By chenyao
what's the version of cufflinks?

what's the version of cufflinks?
Forum: Bioinformatics 08-31-2011, 07:49 AM
Replies: 6
Views: 5,551
Posted By chenyao
I figure out: using grep -w or awk. Another...

I figure out: using grep -w or awk.

Another question : lots of reads (mapping quality=0) are aligned to reapeted region in my RNA-seq data. what does this mean?
Forum: Bioinformatics 08-31-2011, 07:34 AM
Replies: 6
Views: 5,551
Posted By chenyao
After checking the results, I found using grep...

After checking the results, I found using grep "XH:i:1" I mistook the reads with "XH:i:1**", see the example:

2045_1360_1504_F5-BC 409 chr7 3155885 0 25M * 0 0 ...
Forum: Bioinformatics 08-31-2011, 03:59 AM
Replies: 6
Views: 5,551
Posted By chenyao
Question on mapping quality and uniquely mapped read

Dear all.

I use tophat to map RNA-seq data. After getting results, I use two ways to filter the alignment. one is using grep "NH:i:1" to get uniquely mapping reads; the other is using samtools...
Forum: Bioinformatics 08-24-2011, 11:17 PM
Replies: 6
Views: 4,925
Posted By chenyao
Smile Thank you so much. So --bowtie-n do not need the...

Thank you so much. So --bowtie-n do not need the number, that's my mistake.
Forum: Bioinformatics 08-24-2011, 07:41 AM
Replies: 6
Views: 4,925
Posted By chenyao
Are you sure? If it is , then there is no...

Are you sure? If it is , then there is no difference between "--initial-read-mismatches" and "--bowtie-n". Why they set two options? And I can't allow the mismatch more than 3? This is unfair for...
Forum: Bioinformatics 08-24-2011, 07:21 AM
Replies: 6
Views: 4,925
Posted By chenyao
No, I did not use bowtie-n when I got this error....

No, I did not use bowtie-n when I got this error. Also, I got the same error even I set the --initial-read-mismatches to 4.
Forum: Bioinformatics 08-24-2011, 02:51 AM
Replies: 6
Views: 4,925
Posted By chenyao
Tophat with --initial-read-mismatches command Error:

Dear all,

I use tophat with --initial-read-mismatches 10

However I have the error:

gzip: stdout: Broken pipe
error:could not open pipe gzip:left_kept.fa.z

----
Forum: Bioinformatics 08-23-2011, 06:43 AM
Replies: 9
Views: 3,582
Posted By chenyao
Thank you. One thing confusing me is the...

Thank you. One thing confusing me is the defination of proper pair. It's a pair read which were aligned with the defined distance (I believe it's the fragment size). However, if the pair reads were...
Forum: Bioinformatics 08-23-2011, 06:06 AM
Replies: 3
Views: 2,337
Posted By chenyao
Thank you, If it's up to 3, the I understand the...

Thank you, If it's up to 3, the I understand the error. Another question is for pair-end reads, such as 50bp*25bp, the mismatch value is the same for both reads. But since the length of reads are...
Forum: Bioinformatics 08-23-2011, 02:18 AM
Replies: 3
Views: 2,337
Posted By chenyao
Wrong of Tophat's bowtie parameters, a bug

Dear all,

I use tophat --bowtie-n 4 to set bowtie mismatch, however, I found the error,

[Tue Aug 23 17:09:09 2011] Beginning TopHat run (v1.3.1)
-----------------------------------------------...
Forum: Bioinformatics 08-22-2011, 05:15 PM
Replies: 9
Views: 3,582
Posted By chenyao
Thank you very much! It's pretty clear. I also...

Thank you very much! It's pretty clear. I also have a question. For pair end reads, what if one read mapped to one exon and the other mapped to the other exon? How define this kind of alignment, is...
Forum: Bioinformatics 08-20-2011, 07:03 PM
Replies: 15
Views: 14,378
Posted By chenyao
How can I get uniquely mapped reads? I konw I can...

How can I get uniquely mapped reads? I konw I can use -q to get realiable reads, but I still want to know how many reads are unique not matter they are paired or not?
Forum: Bioinformatics 08-19-2011, 06:41 PM
Replies: 9
Views: 3,582
Posted By chenyao
Thank you. That's exactly my question. Why reads...

Thank you. That's exactly my question. Why reads contiguously align to the genome can define a exon? How define "congiguous" ?
Forum: Bioinformatics 08-19-2011, 09:03 AM
Replies: 15
Views: 14,378
Posted By chenyao
It's a pair-end data, how about one read mapped...

It's a pair-end data, how about one read mapped and the other not. Did -F 4 will retain the mapped reads without considering mate? If so , how can I extract paired mapping reads?
Forum: Bioinformatics 08-19-2011, 08:32 AM
Replies: 20
Views: 7,241
Posted By chenyao
Thank you. So as marcowanger said, the missing...

Thank you. So as marcowanger said, the missing base "." should be after the "T". I will check it.
Forum: Bioinformatics 08-19-2011, 08:23 AM
Replies: 9
Views: 3,582
Posted By chenyao
Any help????

Any help????
Forum: Bioinformatics 08-19-2011, 08:17 AM
Replies: 15
Views: 14,378
Posted By chenyao
I am not sure -F 4 will get mapped reads. -F...

I am not sure -F 4 will get mapped reads.

-F will skip alignments with bits present in INT,

4 is the unmapped reads?
Forum: Bioinformatics 08-18-2011, 11:24 PM
Replies: 9
Views: 3,582
Posted By chenyao
Naive question about read mapping, where is intron in genome.fa data

Dear all.

I have a question. I found the genome fastq data only contained sequence "ATCGG...", How the mapping softwre, such as tophat, decide where is the intron or exon?
Forum: Bioinformatics 08-18-2011, 05:48 AM
Replies: 16
Views: 2,748
Posted By chenyao
see wiki: ...

see wiki:
http://en.wikipedia.org/wiki/Normal_distribution.

for simple, you can plot your data to see if it is symmetric and bell-shaped.

but I doult it, most data didn't obey it. But it's...
Forum: Bioinformatics 08-18-2011, 05:36 AM
Replies: 16
Views: 2,748
Posted By chenyao
It's very simple, much more than deseq. you...

It's very simple, much more than deseq.

you can use "sam" or "dchip" module.

It depends on the distribution of your data. If it's normal distribution, the simplest method is t-test.
Forum: Bioinformatics 08-18-2011, 05:16 AM
Replies: 16
Views: 2,748
Posted By chenyao
Do you know "R"? It has many tools to...

Do you know "R"?

It has many tools to use.
Forum: Bioinformatics 08-18-2011, 05:11 AM
Replies: 16
Views: 2,748
Posted By chenyao
You can try sam method, or moderated t-test

You can try sam method, or moderated t-test
Forum: Bioinformatics 08-18-2011, 05:08 AM
Replies: 2
Views: 7,426
Posted By chenyao
truly, the awk command can not generate 'bam'...

truly, the awk command can not generate 'bam' file, you can try making 'san' file then convert to bam file by samtools, but I am not sure it can work.
Forum: Bioinformatics 08-17-2011, 07:00 PM
Replies: 20
Views: 7,241
Posted By chenyao
I don't know. It's a color-space data. I tried to...

I don't know. It's a color-space data. I tried to transfer it to fastq by "solid2fa", but it seems failed, the data become to:

@1_15_97
T12310123033313323122113012323023202122223322003122
+...
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