SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 20 of 20
Search took 0.00 seconds.
Search: Posts Made By: kalyankpy
Forum: Epigenetics 11-04-2014, 12:31 AM
Replies: 2
Views: 1,400
Posted By kalyankpy
You may get fine tuned answers if you could let...

You may get fine tuned answers if you could let the community know what is the environment you are familiar with. For eg., Are you looking for annotation tools in R or PERL or commandline based tools!
Forum: Epigenetics 10-22-2014, 01:40 AM
Replies: 53
Views: 7,335
Posted By kalyankpy
Welcome to the R world! I do not have a straight...

Welcome to the R world! I do not have a straight forward answer for you. But I share my personal experience of working with a specific package with out knowledge of R

My experience with R started...
Forum: Sample Prep / Library Generation 10-20-2014, 06:40 AM
Replies: 13
Views: 2,599
Posted By kalyankpy
I have looked at your bioanalyzer plots. I...

I have looked at your bioanalyzer plots. I noticed your previous working ChIP library and compared it with your present PCR amplified library. In my opinion all your reagents are working fine and...
Forum: Sample Prep / Library Generation 10-19-2014, 03:25 AM
Replies: 13
Views: 2,599
Posted By kalyankpy
I regularly do NGS library prep and routinely use...

I regularly do NGS library prep and routinely use AMPure beads. In my experience I have always noticed that library size increases by 120 bp upon PCR and smaller fragments from the sonication amplify...
Forum: Academic/Non-Profit Jobs 09-25-2014, 05:40 AM
Replies: 0
Views: 1,077
Posted By kalyankpy
Postdoctoral position in epigenome bioinformatics at UTU, Finland

Epigenomics Laboratory (Hawkins Lab)

The Epigenomics Group at the Turku Centre for Biotechnology has an available Postdoctoral position for a computational biologist to specialize in epigenomic...
Forum: Bioinformatics 01-02-2014, 10:13 PM
Replies: 649
Views: 173,396
Posted By kalyankpy
Dear Chris, Easiest way to move from Bismark...

Dear Chris,

Easiest way to move from Bismark to Methylkit is to use the .sam file from alignment as input for Methylkit.

In the other case one has to extract methylation data from .sam file and...
Forum: Bioinformatics 06-23-2012, 03:13 AM
Replies: 649
Views: 173,396
Posted By kalyankpy
@kshankar It is not uncommon to find reads...

@kshankar

It is not uncommon to find reads that doesnt start with CGG or TGG. However, observing only 30% of reads with CGG or TGG as starting triplet is of concern. In our experience we also...
Forum: Epigenetics 11-30-2011, 06:19 AM
Replies: 57
Views: 35,935
Posted By kalyankpy
Which nucleotide to Add

Hi Phillip,

I dont have a definite answer for you. All I can say is our library worked perfectly fine with just Klenow! It is interesting for me to know if someone knows the answer for your...
Forum: Epigenetics 11-30-2011, 06:00 AM
Replies: 57
Views: 35,935
Posted By kalyankpy
ChIP-Seq protocol

Hi Ethanol,

Thanks for sharing the protocol. I noticed that you are doing end repair and A-tailing in two steps. We have a shortened protocol that combines end repair and A-tailing for this part...
Forum: Epigenetics 11-30-2011, 05:30 AM
Replies: 57
Views: 35,935
Posted By kalyankpy
Share the protocol

Dear Ethanol,

We also tried a chip-seq with trueseq kit without much success. Can u share the protocol with us!

Kalyan
Forum: Bioinformatics 11-30-2011, 05:02 AM
Replies: 6
Views: 3,433
Posted By kalyankpy
Cutadapt

I have used Cutadapt (code.google.com/p/cutadapt/). I liked this tool as it allows user to define and fine tune each of the parametre. You can also allow errors in identifying the adapters. If in...
Forum: Bioinformatics 11-23-2011, 08:56 AM
Replies: 10
Views: 5,426
Posted By kalyankpy
CASAVA .bcl to fastq output

Hi,

We have a control run on new HiSeq Machine installed recently. The fastq files extracted from CASAVA 1.8.2 has a different format (Pasted below)


@HWI-ST1072:144:D0BVUACXX:2:1101:1242:2124...
Forum: Bioinformatics 11-19-2011, 09:11 AM
Replies: 29
Views: 17,571
Posted By kalyankpy
Installation problem in CASAVA1.8.2

Hi,

I have faced the same problem while configuring the CASAVA1.8.2 on Ubuntu 11.10 (64bit). After going through this thread I followed the same strategy to copy the libz.so and libpthread* to...
Forum: Illumina/Solexa 11-16-2011, 03:08 AM
Replies: 7
Views: 4,489
Posted By kalyankpy
RRBS sequencing!

Dear Felix,

I have prepared RRBS libraries recently (My first NGS library) and am waiting for data! Meanwhile I downloaded K562-rep2 (Myers lab RRBS data) to practise data analysis and understand...
Forum: Epigenetics 11-07-2011, 04:44 AM
Replies: 35
Views: 12,618
Posted By kalyankpy
Fix to the ubuntu installation of BSMAP

Hi,

Yes finally the problem is solved. Here I explain the steps that help me resolve the installation steps in Ubuntu 11.04

tweak the makefile in the bsmap directory as follows

original line...
Forum: Epigenetics 11-01-2011, 06:46 AM
Replies: 35
Views: 12,618
Posted By kalyankpy
Hi, The problem still xists. I dont know if my...

Hi, The problem still xists. I dont know if my message is clear for you. I could successfully install SAMTOOLS as a standalone application. However, I fail to install it when it is part of bsmap....
Forum: Epigenetics 10-31-2011, 11:20 PM
Replies: 35
Views: 12,618
Posted By kalyankpy
BSMAP installation on ubuntu

Hi Yuanxin,

I went through the link suggested by you! I noticed that there was a bug in the samtools in earlier versions which was rectified after 0.1.13 version (I noticed that the samtools you...
Forum: Epigenetics 10-28-2011, 09:03 AM
Replies: 35
Views: 12,618
Posted By kalyankpy
Hi Yuanxin, I am quite interested in BSMAP....

Hi Yuanxin,

I am quite interested in BSMAP. I am working on RRBS data from stem cells. I am trying to install BSMAP on my computer (Ubuntu 11.10, 64 bit). But it stops with an error. I posted the...
Forum: Bioinformatics 04-04-2011, 07:59 AM
Replies: 11
Views: 8,745
Posted By kalyankpy
Hi Bjorn, In my case there wasnt any problem...

Hi Bjorn,

In my case there wasnt any problem in the data. Rather when I uninstalled the ....24 version of the blast++ and worked with 23 version things worked out pretty smooth. Later I noticed...
Forum: Bioinformatics 03-20-2011, 10:18 PM
Replies: 11
Views: 8,745
Posted By kalyankpy
Exclamation Blast database creation : Error

HI,

I am new to Bioinformatics. I am creating a database with the fasta formatted sequences from high througput sequncing data (20-30 bp in length). While I create the blast database (version...
Showing results 1 to 20 of 20

 


All times are GMT -8. The time now is 01:45 PM.


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