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Forum: Bioinformatics 06-16-2014, 10:58 PM
Replies: 1
Views: 1,715
Posted By bnfoguy
Post Bedtools Intersection files

Hello,

I have a Splice Junction file in the tab delimited format and it looks like this:


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1 hour ago by
ruchiksy 0
Singapore
Forum: Introductions 02-11-2014, 08:06 PM
Replies: 3
Views: 1,253
Posted By bnfoguy
Post Graduate School Advice

Hello,

I am currently applying to M.Sc. programs in Bioinformatics and so far I have been accepted at the University of Saarland in Germany and the Bonn-Aachen International Center for Technology...
Forum: Bioinformatics 07-12-2012, 08:30 AM
Replies: 1
Views: 1,987
Posted By bnfoguy
Question Parsing a VCF file for indels

Hello,

I am new to Python and and I am trying to parse a VCF file that has reads containing the flag "INDEL". I want to extract these flag lines into a new VCF file using a Python script. I just...
Forum: Bioinformatics 07-06-2012, 10:00 AM
Replies: 2
Views: 1,464
Posted By bnfoguy
This is the output I get after running the...

This is the output I get after running the mergeoutputdiploid command:

[ryajnik@bayes dindel-1.01-python]$ ./mergeOutputDiploid.py --inputFiles...
Forum: Academic/Non-Profit Jobs 06-30-2012, 06:46 PM
Replies: 0
Views: 1,186
Posted By bnfoguy
Looking for an Entry Level position

Hello,

I am looking to work in an entry level position in an academic research group or industry lab. I have 4 years of research at the undergraduate level and am proficient in using Perl and...
Forum: Bioinformatics 06-26-2012, 09:20 AM
Replies: 2
Views: 1,464
Posted By bnfoguy
Exclamation Dindel Realining Reads

Hello,

I am using to call indels from cancer data. So far I have been successfull with Stage 1, 2 & 3. When I try to use the mergeOutpuDiploid in stage 4, I get the following error:

...
Forum: Bioinformatics 06-25-2012, 06:58 AM
Replies: 8
Views: 10,339
Posted By bnfoguy
Exclamation CIGAR and Sequence length incosistent

Hello,

I am trying to convert a .sam file into .bam file and I get the following error:

CIGAR and Sequence length are inconsistent. Below is the offending line:

ERR035488.960541 147 ...
Forum: Bioinformatics 06-24-2012, 08:49 AM
Replies: 1
Views: 1,689
Posted By bnfoguy
Exclamation Errors in mapping cancer exome data

I am trying to map the reads from the ERP000703 study (http://www.ncbi.nlm.nih.gov/sra/ERX013480). I am using stampy to do the paired end mapping and when I execute the script with the following...
Forum: Bioinformatics 06-19-2012, 06:31 AM
Replies: 1
Views: 6,085
Posted By bnfoguy
Exclamation Converting .sam to .vcf

I have some files in the .sam format which I obtained after I ran Stampy on some Cancer reads. I now have to convert the .sam files to .vcf files to do some analysis and am clueless on how to do the...
Forum: Bioinformatics 03-07-2012, 12:19 PM
Replies: 0
Views: 1,816
Posted By bnfoguy
Arrow Software/code for motif collection

I am working on a project that require me to write code that will detect tertiary RNA motifs like A Minors. Is there any software or code that will be able to do this?

Thank you
Forum: Bioinformatics 09-09-2011, 08:10 AM
Replies: 0
Views: 1,706
Posted By bnfoguy
Exclamation Using Tabix for parsing files

Hello,

I am trying to access a huge file that I downloaded from 1K Genomes and I put it on my portable HDD. I have managed to use the Ubuntu shell to get to the HDD location but how do I use Tabix...
Forum: Bioinformatics 06-13-2011, 06:04 PM
Replies: 0
Views: 1,614
Posted By bnfoguy
Question Mapping reference genome to ensembl identifier

I am trying to map ensembl identifiers to the reference genome GRCh 37. I am kind of confused as to which database to access for this. The file in question is...
Forum: Bioinformatics 06-06-2011, 01:27 PM
Replies: 15
Views: 9,173
Posted By bnfoguy
Hello BAMseek, Thanks for your suggestions....

Hello BAMseek,

Thanks for your suggestions. I will try these and let you know if I have any success. Would you know of a method to read the .tbi file? Like opening it with notepad or any other...
Forum: Academic/Non-Profit Jobs 06-02-2011, 03:13 PM
Replies: 15
Views: 6,538
Posted By bnfoguy
Biology/Bioinformatics Ph.D.

Hello,

I am a third year undergrad majoring in Bioinformatics. I have had over two years experience in a Stem Cell research lab and now I have taken up a real bioinformatics research project on...
Forum: Bioinformatics 06-01-2011, 07:44 AM
Replies: 15
Views: 9,173
Posted By bnfoguy
Thanks for your reply, I have manually...

Thanks for your reply,

I have manually extracted the file but as you said the traditional text editors like Notepad or Word are having trouble opening the file due to its size. Is there a way that...
Forum: Bioinformatics 05-31-2011, 02:46 PM
Replies: 15
Views: 9,173
Posted By bnfoguy
Question Accessing .vcf.gz files on a Windows platform

Hello,

I'm a first timer to bioinformatics research and have recently been working on a project involving genetic variations. I am supposed to use the latest 1k genomes release file which is...
Forum: Introductions 05-31-2011, 02:39 PM
Replies: 373
Views: 145,653
Posted By bnfoguy
Hello SEQanswers community! I am a third...

Hello SEQanswers community!

I am a third year undergrad from New Jersey, USA. I'm currently working on a Genetic Variations project. I'm still learning the ropes and hope to find guidance from...
Showing results 1 to 17 of 17

 


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