SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 29
Search took 0.00 seconds.
Search: Posts Made By: harryzs
Forum: Bioinformatics 10-18-2013, 12:19 AM
Replies: 4
Views: 1,102
Posted By harryzs
There is a tool from picard ...

There is a tool from picard
http://picard.sourceforge.net/explain-flags.html

use the number at second column (e.g. for the first read: 141 )
Forum: Bioinformatics 10-16-2013, 01:47 AM
Replies: 6
Views: 2,656
Posted By harryzs
I don't think you need to install Galaxy. ...

I don't think you need to install Galaxy.


A user only needs to write a very small configuration file, telling the program which samples to look at and how they should be combined with different...
Forum: Bioinformatics 10-15-2013, 07:57 AM
Replies: 6
Views: 2,656
Posted By harryzs
try ngsplot ...

try ngsplot

https://code.google.com/p/ngsplot/
Forum: Genomic Resequencing 10-09-2013, 02:10 AM
Replies: 8
Views: 3,029
Posted By harryzs
-->(howto) Perform local realignment around...

-->(howto) Perform local realignment around indels
Forum: Genomic Resequencing 10-09-2013, 02:09 AM
Replies: 8
Views: 3,029
Posted By harryzs
You may follow this ...

You may follow this
http://www.broadinstitute.org/gatk/guide/topic?name=tutorials
Forum: Bioinformatics 10-08-2013, 01:10 PM
Replies: 12
Views: 11,828
Posted By harryzs
Thumbs up Great. Thank you very much for sharing.

Great. Thank you very much for sharing.
Forum: Bioinformatics 10-08-2013, 12:09 PM
Replies: 12
Views: 11,828
Posted By harryzs
May I ask a question: for H3K27me3 (human/mouse),...

May I ask a question: for H3K27me3 (human/mouse), how many reads (depth) do we need to get "good" results, according to your experiences?
Forum: Bioinformatics 10-08-2013, 07:58 AM
Replies: 12
Views: 11,828
Posted By harryzs
Just a reminder, if you can wait for two months,...

Just a reminder, if you can wait for two months, you will know how people (Anshul) from ENCODE do with broad peaks stably.

https://groups.google.com/forum/#!topic/macs-announcement/yG8M8Sx_eTM
Forum: Bioinformatics 10-05-2013, 04:46 AM
Replies: 20
Views: 6,819
Posted By harryzs
One vote for you

One vote for you
Forum: Bioinformatics 10-05-2013, 01:27 AM
Replies: 8
Views: 4,306
Posted By harryzs
I checked unmapped.bam from TopHat 2.0.9 ...

I checked unmapped.bam from TopHat 2.0.9

samtools view -f 0x200 unmapped.bam | head

I got:
...
Forum: Bioinformatics 10-04-2013, 06:55 AM
Replies: 12
Views: 3,275
Posted By harryzs
Just do what I did run: ${path_to_bwa}/bwa...

Just do what I did

run: ${path_to_bwa}/bwa

path_to_bwa = where you exectued the 'make' command
Forum: Bioinformatics 10-04-2013, 05:44 AM
Replies: 12
Views: 3,275
Posted By harryzs
If I Just run ${path_to_bwa}/bwa I get...

If I Just run
${path_to_bwa}/bwa

I get following message :
----------------------------------
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.5a-r405
Contact: Heng...
Forum: Bioinformatics 10-04-2013, 04:09 AM
Replies: 12
Views: 3,275
Posted By harryzs
please show us what you got after running 'make'

please show us what you got after running 'make'
Forum: Bioinformatics 10-04-2013, 02:20 AM
Replies: 8
Views: 7,969
Posted By harryzs
Yes. I agree. See how people from ENCODE are...

Yes. I agree.
See how people from ENCODE are doing:
samtools view -b -F 1548 -q 30 chipSampleRep1.bam

they(Anshul Kundaje) use -q 30 in their guideline.
...
Forum: Bioinformatics 10-03-2013, 12:40 PM
Replies: 2
Views: 1,651
Posted By harryzs
Yes, Tao has already confirmed this: ...

Yes, Tao has already confirmed this:
https://groups.google.com/forum/#!searchin/macs-announcement/paired$20end|sort:date/macs-announcement/J9vbZz4s3BM/KKVWRXl24CYJ


----By Tao:
Both MACS14 and...
Forum: Bioinformatics 09-30-2013, 06:18 AM
Replies: 3
Views: 3,689
Posted By harryzs
"GATK accept interval files for processing...

"GATK accept interval files for processing subsets of the genome in Picard-style interval lists"
http://www.broadinstitute.org/gatk/guide/article?id=1204

I think you just need to change your bed...
Forum: RNA Sequencing 08-13-2012, 02:25 AM
Replies: 6
Views: 9,368
Posted By harryzs
Just a reminder, if you did not see this: ...

Just a reminder, if you did not see this:

http://tophat.cbcb.umd.edu/faq.html
Forum: General 06-25-2012, 12:43 AM
Replies: 1
Views: 2,187
Posted By harryzs
Hi, Please read this ...

Hi,
Please read this
http://ethanomics.wordpress.com/2011/08/07/how-to-compare-transcription-factor-binding-between-two-chip-seq-samples/


You may also need to look at DiffBind from...
Forum: Bioinformatics 06-16-2012, 01:45 AM
Replies: 5
Views: 1,546
Posted By harryzs
Just try cufflinks 2.0.1

Just try cufflinks 2.0.1
Forum: RNA Sequencing 05-23-2012, 12:15 AM
Replies: 16
Views: 5,133
Posted By harryzs
Sorry, I have no idea about this. You may post...

Sorry, I have no idea about this.
You may post your question here :
http://seqanswers.com/forums/forumdisplay.php?f=18
Forum: RNA Sequencing 05-22-2012, 02:24 PM
Replies: 16
Views: 5,133
Posted By harryzs
Just remove --solexa1.3-quals and try. My...

Just remove --solexa1.3-quals and try.

My data are also from Illumia Hi-seq, and without --solexa1.3-quals, everything is fine with tophat v2.0.1
Forum: Bioinformatics 02-08-2012, 08:51 AM
Replies: 7
Views: 2,558
Posted By harryzs
please see this ...

please see this
https://groups.google.com/group/macs-announcement/browse_thread/thread/9e401eeced7ba235/fd65a20b720a437c?lnk=gst&q=to-small#fd65a20b720a437c
"....
By default, MACS will now scale...
Forum: Bioinformatics 02-08-2012, 06:45 AM
Replies: 7
Views: 2,558
Posted By harryzs
in README of MACS1.4 --to-small ...

in README of MACS1.4

--to-small When set, scale the larger dataset down to the smaller
dataset, by default, the smaller dataset will be
...
Forum: Bioinformatics 02-02-2012, 12:48 AM
Replies: 7
Views: 1,801
Posted By harryzs
you should first tell us what kind of data you...

you should first tell us what kind of data you have??

NGS data for ChiP-seq, RNA-seq?

or

see this http://seqanswers.com/forums/showthread.php?t=6854&highlight=duplicates+chip-seq
Forum: Bioinformatics 01-31-2012, 03:55 AM
Replies: 4
Views: 6,105
Posted By harryzs
I agree. see this...

I agree.

see this http://seqanswers.com/forums/showthread.php?t=6854&highlight=duplicates
Showing results 1 to 25 of 29

 


All times are GMT -8. The time now is 09:48 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO