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Search: Posts Made By: lewewoo
Forum: Core Facilities 10-24-2015, 09:18 AM
Replies: 2
Views: 5,944
Posted By lewewoo
Illumina NextSeq vs. HiSeq4000

NextSeq is good for small RNA libraries?
Any systematic comparison of both systems?
Forum: Bioinformatics 05-15-2013, 10:08 AM
Replies: 16
Views: 5,099
Posted By lewewoo
I think some people (or all) should mention this...

I think some people (or all) should mention this issue to Nature editors as comments or letter to editors. It is important to include codes in the paper upon published. All high end journal requests...
Forum: Bioinformatics 04-09-2013, 09:01 AM
Replies: 0
Views: 926
Posted By lewewoo
SNP filtering

I had a list of interesting SNPs from tumor samples, I am wondering how I can remove the SNP associated with population identified through HapMap or 1000 Genomes. I would like to pick one of the...
Forum: Bioinformatics 03-19-2013, 06:20 AM
Replies: 7
Views: 2,849
Posted By lewewoo
Thanks! I will try it for sure!

Thanks!
I will try it for sure!
Forum: Bioinformatics 03-18-2013, 05:05 PM
Replies: 7
Views: 2,849
Posted By lewewoo
closest TSS of given peaks

Hi I have a list of ChipSeq peaks, what are the fastest way to find the closest TSS in the given length (for example, 1kb, 2kb... 10kb); Any tools or Perl scripts for this? Thanks a lot!
Forum: Bioinformatics 11-05-2012, 10:15 AM
Replies: 0
Views: 815
Posted By lewewoo
Insert size and library quality

Why people care about insert size and the standard deviation? How it reflects the quality of the libraries. Thanks!
Forum: Bioinformatics 09-11-2012, 05:11 AM
Replies: 2
Views: 1,091
Posted By lewewoo
Thanks! : )

It is helpful!
Forum: Bioinformatics 09-10-2012, 08:15 AM
Replies: 2
Views: 1,091
Posted By lewewoo
Intergenic reads

Hi, I am going to count and summarize the intergenic reads, please help with:
1) how to define intergenic regions;
2) how to define intergenic regions using GenomicFeatures (R package)
3) Thanks!...
Forum: Bioinformatics 09-03-2012, 06:37 AM
Replies: 3
Views: 2,691
Posted By lewewoo
thanks

will try it:)
Forum: Bioinformatics 09-02-2012, 08:56 PM
Replies: 3
Views: 2,691
Posted By lewewoo
How to get sequence from hg19.fa

If I have sequence start and end coordinates, how can I get the sequence from local hg19.fa file. Either using samtools or perl will be good for me.
hg19 has been indexed using samtools.
Thanks!
Forum: Bioinformatics 08-29-2012, 07:53 AM
Replies: 1
Views: 1,075
Posted By lewewoo
Samtools mpileup all variance report parameters

Hi, I am a beginner working on SNP callings. I am trying samtools mpileup and it works pretty cool. However, I have no idea about the parameters and I am thinking which parameters control the output...
Forum: Bioinformatics 04-03-2012, 02:52 PM
Replies: 2
Views: 9,810
Posted By lewewoo
Thanks! Just double check the packages are: ...

Thanks!
Just double check the packages are:
GenomicRanges
rtracklayer
Forum: Bioinformatics 03-26-2012, 02:15 PM
Replies: 12
Views: 10,052
Posted By lewewoo
HugeSEQ: a good pipeline

Maybe my tread is silly, however, I did not get anybody helping me out. I can easily ran Samtools mpileup or GATK, but I really want to get something information as for the parameter setting-up and...
Forum: Bioinformatics 02-20-2012, 03:41 PM
Replies: 12
Views: 10,052
Posted By lewewoo
SNP calling and allele specific expression by RNAseq

Any solid and reliable pipeline for this application?
I would like to use Samtools pile-up and some stat steps, but would like to have the helps for a reliable pipeline established well. Any help...
Forum: Bioinformatics 11-16-2011, 05:57 PM
Replies: 2
Views: 9,810
Posted By lewewoo
GFF to GTF, and GTF to GRanges objects

1) how to transfer GFF to GTF; human genome;

2) how to make GRanges objects using GTF files.

Thanks a lot!
Forum: Bioinformatics 11-16-2011, 05:56 PM
Replies: 2
Views: 2,206
Posted By lewewoo
Cufflinks FPKM inconsistent with reads in IGV

I have 6 samples the FPKM is as following:
0 0 0.23 0.15 0.56 0.3

however, when I used IGV to double checked the reads mapped, there are a lot of reads and the amounts mapped in the...
Forum: Illumina/Solexa 11-15-2011, 06:10 AM
Replies: 24
Views: 9,242
Posted By lewewoo
so that means this poor quality is not caused by...

so that means this poor quality is not caused by RTA? I have this concern because the Illumina manual said RTA may cause some errors.
Yes I have all the .cft files and cycles lanes... everything......
Forum: Illumina/Solexa 11-14-2011, 09:00 PM
Replies: 24
Views: 9,242
Posted By lewewoo
Thanks for the advice! I read about this on the...

Thanks for the advice! I read about this on the illumina manual and it will also be great if someone can share in field experience about this...

Fortunately, the majority of the reads was...
Forum: Illumina/Solexa 11-14-2011, 06:43 PM
Replies: 24
Views: 9,242
Posted By lewewoo
CASAVA extracted fastq, however, there is a...

CASAVA extracted fastq, however, there is a folder called:
Undetermined_indices
it contains fastq files also; basically, how many reads in this folder? how big about this folder? any quality...
Forum: Illumina/Solexa 11-14-2011, 05:52 PM
Replies: 2
Views: 1,964
Posted By lewewoo
Thanks a lot! Tophat said "-r" is an expected...

Thanks a lot!
Tophat said "-r" is an expected number, that means Tophat just requires a "-r" number to estimate the mean number and your script could do a better measurement for the mean, right?...
Forum: Illumina/Solexa 11-14-2011, 02:36 PM
Replies: 2
Views: 1,964
Posted By lewewoo
Help about setting up TopHat

The sequencing people in house told us that the library fragments range from 200-500 bp with a major band at ~280bp, so for tophat setting, how could we set up -r? we have 100 cycles for read1 and...
Forum: Illumina/Solexa 11-14-2011, 02:31 PM
Replies: 24
Views: 9,242
Posted By lewewoo
ultimate solution: super power servers!

ultimate solution: super power servers!
Forum: Bioinformatics 11-13-2011, 12:35 PM
Replies: 7
Views: 2,795
Posted By lewewoo
no, i did not see that, can you post all the...

no, i did not see that, can you post all the command and response message here? maybe can know what happened...
Forum: Bioinformatics 11-13-2011, 07:38 AM
Replies: 7
Views: 2,795
Posted By lewewoo
my solution is waiting....if the terminal window...

my solution is waiting....if the terminal window is still working, do nothing just wait.... other samples only 2hours, this sample needs overnight...dont know why .... good luck!
Forum: Illumina/Solexa 11-11-2011, 08:29 PM
Replies: 24
Views: 9,242
Posted By lewewoo
Thanks guys, This is the first time for us to...

Thanks guys,
This is the first time for us to convert .bcl to fastq, not too much experience, but soon will improve computing ability; just a little updating what we have and what I am doing, maybe...
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