SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 36
Search took 0.06 seconds.
Search: Posts Made By: henry
Forum: Bioinformatics 11-26-2009, 04:40 PM
Replies: 7
Views: 7,099
Posted By henry
Bwa replaces Ns in the human genome from NCBI...

Bwa replaces Ns in the human genome from NCBI build 36 with A,C,G,T randomly. Bowtie by default excludes Ns.

As for hg18 in UCSC, there are lower-case letters for representing repeat regions in...
Forum: Bioinformatics 11-26-2009, 01:55 AM
Replies: 7
Views: 7,099
Posted By henry
how bwa and bowtie handle repeats?

hg18 downloaded from ucsc consits of lower-case letters like a c g t.
human build 36 downloaded from ncbi consits of A C G T N.

Could anyone kindly tell me how bwa and bowtie deal with the Ns and...
Forum: Bioinformatics 11-08-2009, 10:41 PM
Replies: 15
Views: 4,919
Posted By henry
Hi Knoto, I didn't try to fix the...

Hi Knoto,

I didn't try to fix the problems. I ran into the problem, and then I left tophat behind. Why not try other applications that can also perform RNA-seq analysis?

Best wishes
...
Forum: Bioinformatics 09-11-2009, 04:05 AM
Replies: 26
Views: 8,393
Posted By henry
Hi Patrick, I only have some experiences...

Hi Patrick,
I only have some experiences (still limited :( ) in dealing with Illumina short reads data.
I got some information from paper named "improved base calling for the illumina...
Forum: Bioinformatics 09-10-2009, 06:55 PM
Replies: 292
Views: 156,399
Posted By henry
With SAMtools, can I extract the number of unique...

With SAMtools, can I extract the number of unique aligned reads, the number of aligned reads with one mismatches, the number of aligned reads with two mismatches?
With SAMtools, can I extract the...
Forum: Bioinformatics 09-10-2009, 06:26 PM
Replies: 1
Views: 2,999
Posted By henry
Smile about bwa aln parameter tuning questions

Hi guys,
I'm using bwa to align solexa short reads (32 bp) to the reference genome. There are a couple of parameters for 'bwa aln', some of which I can't understand well. Could someone kindly...
Forum: Bioinformatics 09-10-2009, 03:48 AM
Replies: 26
Views: 8,393
Posted By henry
Hi patrick, you are welcome. Good luck to...

Hi patrick,
you are welcome. Good luck to your research.

Best

Jing
Forum: Bioinformatics 09-09-2009, 05:24 PM
Replies: 26
Views: 8,393
Posted By henry
Whole genome sequencing of breast carcinoma...

Whole genome sequencing of breast carcinoma sample can help us identify breast-carcinoma specific SNPs and indels. Among these identified SNPs and indels, there may be some novel mutations. Whether...
Forum: Bioinformatics 09-09-2009, 03:46 AM
Replies: 9
Views: 12,157
Posted By henry
This is a good question. I also wanna know. could...

This is a good question. I also wanna know. could anyone kindly help us?
Btw, how much time did it take to denovo assemble more than 100 million reads into contigs?

Best

Jing
Forum: Bioinformatics 09-09-2009, 03:38 AM
Replies: 26
Views: 8,393
Posted By henry
You mean you wanna obtain statistical data on...

You mean you wanna obtain statistical data on which bioinformatics tools have been used among the previous breast cancer researches?
Forum: Bioinformatics 09-09-2009, 02:30 AM
Replies: 26
Views: 8,393
Posted By henry
Hi Partrick, How would you like to...

Hi Partrick,
How would you like to investigate breast cancer? First, we need to determine how we will investigate tumor, like from DNA level, RNA level, protein level, or from angle of...
Forum: Bioinformatics 09-09-2009, 01:08 AM
Replies: 1
Views: 1,725
Posted By henry
i'm trying running bwa samse without setting -n....

i'm trying running bwa samse without setting -n. Thank hl3. ^ ^
Forum: Bioinformatics 09-09-2009, 12:45 AM
Replies: 292
Views: 156,399
Posted By henry
hi, lh3, I ran ./bwa samse -n 255 ref.fa ...

hi, lh3,
I ran ./bwa samse -n 255 ref.fa tissue.sai tissue.fastq> tissue.sam
I will try bwa without setting -n.
Thank you for your help.

Best

Jing
Forum: Bioinformatics 09-09-2009, 12:29 AM
Replies: 1
Views: 1,725
Posted By henry
Smile about problems run into for samtools

Hi,guys,
I created tissue.sam file, using ./bwa samse. I tried to convert the tissue.sam file into tissue.bam, using ./samtools view -bt ref.fa.fai -o tissue.bam tissue.sam
But an error...
Forum: Bioinformatics 09-09-2009, 12:17 AM
Replies: 292
Views: 156,399
Posted By henry
I also ran into the almost the same problem. I'm...

I also ran into the almost the same problem. I'm still stuck with it. I got sam from bwa samse. I created ref_list.fai file using samtools faidx on ref.fa. However errors popped up as follows:
...
Forum: Bioinformatics 09-08-2009, 09:16 PM
Replies: 26
Views: 8,393
Posted By henry
Hi Patrick, At present, we mainly focus...

Hi Patrick,

At present, we mainly focus on oncogenesis, hoping to identify potential drug target. What are your research interests?

Best

Jing
Forum: Bioinformatics 09-08-2009, 06:02 PM
Replies: 26
Views: 8,393
Posted By henry
Hi, Patrick You are welcome. Surely, we can...

Hi, Patrick
You are welcome. Surely, we can share a lot of experiences in processing and analyzing data cohorts. All people can benefit from communications. ^ ^

Best

Jing
Forum: Bioinformatics 09-08-2009, 05:43 PM
Replies: 5
Views: 12,755
Posted By henry
hi mingkunli, Thank you for sharing this....

hi mingkunli,

Thank you for sharing this. ^ ^

Best

Jing
Forum: Bioinformatics 09-08-2009, 03:48 AM
Replies: 5
Views: 12,755
Posted By henry
Sorry, I just misunderstood you. In MAQ, two best...

Sorry, I just misunderstood you. In MAQ, two best hits are kept in the queue for one end. if there are multiple consistent hit pairs, the mapping qualities are set much lower. so suboptimal hits are...
Forum: Bioinformatics 09-08-2009, 03:26 AM
Replies: 5
Views: 12,755
Posted By henry
I haven't used bwa to process paired-end reads....

I haven't used bwa to process paired-end reads. So I have no hand-on experiences yet.
"BWA first finds the positions of all the good hits, sorts them according to the chromosomal coordinates and...
Forum: Bioinformatics 09-08-2009, 02:53 AM
Replies: 5
Views: 12,755
Posted By henry
.sai file is the output of command aln. .sai...

.sai file is the output of command aln. .sai file contain the suffix array coordinate of all short reads loaded in. For bwa, sequence alignment is equal to searching for suffix array interval of...
Forum: Bioinformatics 09-08-2009, 02:36 AM
Replies: 26
Views: 8,393
Posted By henry
Hi, patrick I'm sorry. I don't have pdf...

Hi, patrick

I'm sorry. I don't have pdf copy of that nature paper. I read the hard copy in the library. Why not ask the corresponding author for that nature paper?

Best

Jing
Forum: Bioinformatics 09-07-2009, 07:31 PM
Replies: 26
Views: 8,393
Posted By henry
Hi, BENM Thank you for sharing paper about...

Hi, BENM
Thank you for sharing paper about structural variation. I'm reading it. I just jumped into next generation sequence research nearly one month ago.
To my knowledge, most majority of...
Forum: Bioinformatics 09-07-2009, 06:43 PM
Replies: 15
Views: 4,919
Posted By henry
Hi, Cole Trapnell, Thank you for kindly...

Hi, Cole Trapnell,
Thank you for kindly responding to me. I keyed in gcc -v, and got all the information about gcc as follows:

Using built-in specs.
Target: x86_64-redhat-linux
Configured...
Forum: Bioinformatics 09-07-2009, 03:35 AM
Replies: 26
Views: 8,393
Posted By henry
There are mutation occuring in some segment of...

There are mutation occuring in some segment of human genome. These mutation can be insertion, deletion and inversion of nucleotide sequences ranging from several bp to huandreds of bps.
There is a...
Showing results 1 to 25 of 36

 


All times are GMT -8. The time now is 02:36 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO