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Forum: Bioinformatics 07-03-2017, 07:56 PM
Replies: 0
Views: 2,042
Posted By discoveradnan
NCBI WGS submission: Need Help

Dear Seniors,
I'm a newbie in field of bioinformatics and learning everything on my own by following tutorials available online. Right now, I'm facing a roadblock in submitting WGS sequences to...
Forum: Bioinformatics 01-17-2016, 04:14 AM
Replies: 1
Views: 1,759
Posted By discoveradnan
Unhappy Facing error while trying to build SNP recalibration model using GATK

Hello everyone,

Kindly help me in fixing following error while trying to build SNP recalibration model uing GATK,

$ java -jar GenomeAnalysisTK.jar -T VariantRecalibrator -R Reference/hg19.fa...
Forum: Bioinformatics 01-06-2016, 06:27 AM
Replies: 3
Views: 1,999
Posted By discoveradnan
Hello etorstenson, Unfortunately I am not...

Hello etorstenson,

Unfortunately I am not being able to download it from the specified address which is http://chgr.mc.vanderbilt.edu/lilab/asap-v1.1.7.tgz. So, can you kindly provide me working...
Forum: Illumina/Solexa 12-16-2015, 12:52 AM
Replies: 1
Views: 806
Posted By discoveradnan
Smile Query about Fastq quality filtering

Hello everyone!!

At the end of Paired end sequencing run from illumina and generation of FASTQ files. Do we need to do quality trimming/filtering by third-party softwares or its already been taken...
Forum: Illumina/Solexa 12-15-2015, 07:36 PM
Replies: 3
Views: 1,104
Posted By discoveradnan
Thanks guys :)

Thanks guys :)
Forum: Illumina/Solexa 12-15-2015, 02:55 AM
Replies: 3
Views: 1,104
Posted By discoveradnan
Confusion regarding output data of paired end sequencing run

Hello everyone!

At the end of the run, for a paired end sequencing, does illumina provides two fastq files for right and left reads or single fastq file in which paired end reads are incorporated?
Forum: Sample Prep / Library Generation 12-13-2015, 09:51 PM
Replies: 0
Views: 906
Posted By discoveradnan
Suggestion needed for using type of water for library prep

Hello everyone! :)

Can you guys kindly suggest that is following water suitable for library preparation and maintenance runs of Illumina MiSeq?

Water
hypotonic, sterile, free from pyrogen
CAS...
Forum: Bioinformatics 12-10-2015, 11:47 PM
Replies: 2
Views: 1,012
Posted By discoveradnan
Thanks a lot GenoMax :)

Thanks a lot GenoMax :)
Forum: Bioinformatics 12-10-2015, 08:50 PM
Replies: 2
Views: 1,012
Posted By discoveradnan
Smile Help required in obtaining NGS data for data analysis practice

Hello everyone!

I'm new to NGS and will be working on data analysis of NGS (Illumina MiSeq) in few months time. So before that, I want to obtain some raw NGS data in FASTQ or FASTA format for some...
Forum: Sample Prep / Library Generation 12-09-2015, 12:38 AM
Replies: 0
Views: 1,498
Posted By discoveradnan
Smile Small confusion regarding microplate shaker usage for

Hello Everyone!

In our lab, we will have to prepare library by using Illumina TruSight Rapid Capture Kit. So, according to its protocol, we need to process samples using High Speed Micro plate...
Forum: Sample Prep / Library Generation 12-04-2015, 08:55 PM
Replies: 0
Views: 1,130
Posted By discoveradnan
Advice needed for shaker usage for illumina library prep kit

Hello Everyone!

In our lab, we will have to prepare library by using Illumina TruSight Rapid Capture Kit. So, according to its protocol, we need to process samples using High Speed Micro plate...
Forum: General 12-04-2015, 08:34 PM
Replies: 2
Views: 1,142
Posted By discoveradnan
nucacidhunter thanks for you reply. I am...

nucacidhunter thanks for you reply.
I am specifically looking for a database from where i can find annotated indels and structural changes of any diseased genes. So that i can design primers...
Forum: General 12-04-2015, 06:42 PM
Replies: 2
Views: 1,142
Posted By discoveradnan
Smile Help needed regarding designing primers

Hello everyone!

I have background knowledge of designing primers but I am facing difficulty in finding a way to design primers specifically for Indels and structural changes of a diseased gene. So...
Forum: Illumina/Solexa 12-03-2015, 07:18 PM
Replies: 6
Views: 3,815
Posted By discoveradnan
Normalization of samples before pooling

Hello everyone!

Can you kindly tell me what is the best way to normalize the samples before pooling? The application I will be working on is screening different diseased genes for mutations.
...
Forum: Illumina/Solexa 12-02-2015, 07:08 PM
Replies: 12
Views: 3,180
Posted By discoveradnan
Thanks a lot jwfoley for being so helpful. :)

Thanks a lot jwfoley for being so helpful. :)
Forum: Illumina/Solexa 12-02-2015, 07:34 AM
Replies: 12
Views: 3,180
Posted By discoveradnan
Jwfoley can you kindly check my sample sheet. I...

Jwfoley can you kindly check my sample sheet. I prepared it according to the protocol I linked. Since Nextera XT adapters and indices are used in this protocol so I also selected same kit for sample...
Forum: Illumina/Solexa 12-01-2015, 08:09 PM
Replies: 12
Views: 3,180
Posted By discoveradnan
Got your point jwfoley. Can you kindly guide me...

Got your point jwfoley. Can you kindly guide me about libraries which are prepared from 2 round PCR? For your reference, I have linked the protocol below.

Does the nextera adapters, P5 and P7...
Forum: Illumina/Solexa 12-01-2015, 09:42 AM
Replies: 12
Views: 3,180
Posted By discoveradnan
Yeah jwfoley, You are right. Those posts must be...

Yeah jwfoley, You are right. Those posts must be about v2 kits.
What about those kits which already include denaturation steps in their library prep protocol? e.g trusight rapid capture or truseq...
Forum: Illumina/Solexa 12-01-2015, 06:59 AM
Replies: 12
Views: 3,180
Posted By discoveradnan
Thanks a lot Jwfoley. This confusion about...

Thanks a lot Jwfoley. This confusion about pooling libraries has been cleared.
I have seen in many posts and literature which recommends diluting library to 8-12pM in a final volume of 600ul for...
Forum: Illumina/Solexa 12-01-2015, 05:54 AM
Replies: 12
Views: 3,180
Posted By discoveradnan
Thanks for your reply Jwfoley. Actually...

Thanks for your reply Jwfoley.
Actually according to truSight rapid capture protocol, In DNA Input Recommendations section on Page 3, it is mentioned that 50ng of total gDNA is recommended per...
Forum: Illumina/Solexa 12-01-2015, 02:58 AM
Replies: 12
Views: 3,180
Posted By discoveradnan
Smile Confusion about Pooling Libraries and Clustering

Hello everyone!


According to TruSight Rapid Capture lib prep method, 50ng (5ng/ul) input DNA is required in a final volume of 10ul for one library. So if we want to pool different libraries...
Forum: Illumina/Solexa 11-25-2015, 11:36 PM
Replies: 2
Views: 2,885
Posted By discoveradnan
Thanks a lot Mike:)

Thanks a lot Mike:)
Forum: Illumina/Solexa 11-24-2015, 09:12 PM
Replies: 2
Views: 2,885
Posted By discoveradnan
Smile A small confusion about Illumina Amplicon Sequencing Protocol

Hello everyone!

I am new to this forum. I will be working very shortly on Illumina MiSeq. So, I am currently trying to understand a protocol for Amplicon Sequencing but facing some confusion in...
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