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Search: Posts Made By: xiangwulu
Forum: Bioinformatics 06-24-2016, 07:45 AM
Replies: 6
Views: 1,399
Posted By xiangwulu
:) Saw it. I think there is no trimming...

:) Saw it.
I think there is no trimming involved at/before that stage. The third file is a collection of unloved ones.
Forum: Bioinformatics 06-24-2016, 07:31 AM
Replies: 6
Views: 1,399
Posted By xiangwulu
Usually, splitting the .sra files of pair-end...

Usually, splitting the .sra files of pair-end reads using fastq-dump from SRA-toolkit,

a parameter --split-3 is used to do this:


Legacy 3-file splitting for mate-pairs: First 2...
Forum: Bioinformatics 06-24-2016, 07:15 AM
Replies: 6
Views: 1,399
Posted By xiangwulu
Thanks your answer. This data can be found...

Thanks your answer.

This data can be found from DRASearch, NCBI SRA, and EBI.
All these sources of these data has strange quality values.
However I wasn't able to find the contact info of the...
Forum: Bioinformatics 06-24-2016, 04:49 AM
Replies: 6
Views: 1,399
Posted By xiangwulu
All sequence bases have the same quality score.

Hi all,
I am doing some analysis on the dataset here:

https://trace.ddbj.nig.ac.jp/DRASearch/experiment?acc=ERX1434776

Some basic info for the data without looking into above link:
----...
Forum: Bioinformatics 03-02-2016, 09:13 AM
Replies: 4
Views: 2,879
Posted By xiangwulu
what does "avgMismatchQuality" mean? does it...

what does "avgMismatchQuality" mean?
does it refer to something with the base quality of mismach base?
Forum: Bioinformatics 03-02-2016, 04:35 AM
Replies: 4
Views: 5,979
Posted By xiangwulu
Thank you for the explanation.

Thank you for the explanation.
Forum: Bioinformatics 03-02-2016, 02:58 AM
Replies: 4
Views: 5,979
Posted By xiangwulu
Thank you.

Thank you.
Forum: Bioinformatics 03-02-2016, 01:03 AM
Replies: 4
Views: 5,979
Posted By xiangwulu
MAPping Quality v.s. Alignment Score (AS) in SAM format

MAPQ: MAPping Quality. It equals −10 log10 Pr{mapping position is wrong}, rounded to the nearest
integer. A value 255 indicates that the mapping quality is not available.

AS i Alignment score...
Forum: Bioinformatics 11-23-2015, 05:58 AM
Replies: 3
Views: 1,214
Posted By xiangwulu
thanks very much.

thanks very much.
Forum: Bioinformatics 11-23-2015, 05:33 AM
Replies: 3
Views: 1,214
Posted By xiangwulu
Non A T G C base in RefSeq zebrafish mRNA sequence

I found some non A T C G base in refseq zebrafish mRNA sequence:
'Y', 'K', 'R', 'M', 'W'

couldn't find out what do they mean.

e.g.
NM_001012366.1...
Forum: Bioinformatics 11-23-2015, 03:42 AM
Replies: 6
Views: 2,086
Posted By xiangwulu
found a solution for my problem. bfast gives...

found a solution for my problem.
bfast gives error when align reads contains non a t c g n base.
Forum: Bioinformatics 11-23-2015, 02:34 AM
Replies: 6
Views: 2,086
Posted By xiangwulu
had similar error too, like the following: ...

had similar error too, like the following:


In function "AlignedEndRead": Fatal Error[ReadFileError]. Variable/Value: a->reads, a->qual, and a->numEntries.
Message: Could not read from file....
Forum: RNA Sequencing 07-24-2015, 07:34 AM
Replies: 0
Views: 757
Posted By xiangwulu
apply Negative Binomial Distribution (NBD) to ribosome profiling data simulation.

Hi,

I want to apply Negative Binomial Distribution to my ribo-seq data simulation process in order to mimic the real data.

The reason of doing this is because I want to compare with the...
Forum: Bioinformatics 03-09-2015, 04:56 AM
Replies: 11
Views: 14,726
Posted By xiangwulu
Hi, I think that we know that the trimming and...

Hi, I think that we know that the trimming and soft-clipping are made for different purposes, but in the SAM file, the cigar string shows the clipping information: e.g. 4S26M but not the reason why...
Forum: Bioinformatics 07-04-2014, 02:51 AM
Replies: 3
Views: 3,410
Posted By xiangwulu
This works, thanks.

This works, thanks.
Forum: Bioinformatics 04-15-2014, 01:53 PM
Replies: 8
Views: 4,333
Posted By xiangwulu
The MD tag in sam files tell something, but not...

The MD tag in sam files tell something, but not enough. Also, some tools does not output MD tag in sam file, like blat, bfast.
Forum: Bioinformatics 04-15-2014, 08:04 AM
Replies: 8
Views: 4,333
Posted By xiangwulu
a fast way to get human genome sequence by coordinate

Hi all,

I want to get a lot human genome fragments (more than 500 million of them) randomly.


This is a partial work of the whole process. I have .sam result file from bowtie, with 10 million...
Forum: Introductions 04-15-2014, 07:53 AM
Replies: 0
Views: 619
Posted By xiangwulu
Hi all,

HI all,
I have just registered today.
Currently I am a PhD research student in Ireland,
My field of study is on parallel computing and bioinformatics.
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