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Search: Posts Made By: Nino
Forum: Bioinformatics 04-20-2015, 06:54 AM
Replies: 7
Views: 2,658
Posted By Nino
@crazyhottommy Try this script. It gives you...

@crazyhottommy

Try this script. It gives you the fastq file instead of the sam/bam file

#!/usr/bin/perl -w ...
Forum: Bioinformatics 04-16-2015, 06:18 AM
Replies: 7
Views: 2,658
Posted By Nino
@GenoMax: I received your PM if you could please...

@GenoMax: I received your PM if you could please look at my response to see if the file I am working on is an alignment file. Also the data I am working with is from NCBI website which I downloaded...
Forum: Bioinformatics 04-14-2015, 06:19 AM
Replies: 7
Views: 2,658
Posted By Nino
Hey were you ever able to find a solution to your...

Hey were you ever able to find a solution to your problem? I am currently running into the same issue as well.

[jhpce01 /amber3/feinbergLab/personal/sramazan/chip-seq]$...
Forum: Bioinformatics 12-15-2014, 11:37 AM
Replies: 0
Views: 1,010
Posted By Nino
Chip-seq RSEG deadzone

Hello,

I am currently using RSEG to do my broad peak calls on my chip-seq data (human). It requires a deadzone bed file based off of the read length of the bam file. I am currently running the...
Forum: Bioinformatics 05-20-2014, 09:44 AM
Replies: 6
Views: 3,957
Posted By Nino
Hey Guys, I am getting this weird error for...

Hey Guys,

I am getting this weird error for my hg19.fa genome file.

this is my command line argument:
genomeCoverageBed -d -i Sample_23430_B14_T.sorted.dedup.rg.resorted.realigned.bed -g...
Forum: Bioinformatics 02-24-2014, 06:14 AM
Replies: 2
Views: 1,559
Posted By Nino
Hey Don, If it was I would have done that...

Hey Don,

If it was I would have done that already but it isn't unfortunately. When using vcf-isec you have to give it more then one file as an argument so it can do the intersection between the ...
Forum: Bioinformatics 02-21-2014, 08:04 AM
Replies: 2
Views: 1,559
Posted By Nino
vcf-isec

Hello,

I understand with vcf-isec you can merge samples were you can output positions present in this many (=), this many or more (+), or this many or fewer (-) files. Is there a program out there...
Forum: Bioinformatics 02-20-2014, 10:24 AM
Replies: 8
Views: 11,011
Posted By Nino
Hello, Would anyone happen to know how to...

Hello,

Would anyone happen to know how to merge a set a vcf files where you have at least 20% to at most 90% of all candidates reported across all files into one new file?

Thanks,
Nino
Forum: Bioinformatics 01-31-2014, 10:41 AM
Replies: 1
Views: 1,396
Posted By Nino
Strand orientation from VCF file

Hello,

I am trying to figure out how I can get the strand orientation of each call made on a snp.vcf file. Does anyone know of a way?

In the end I am looking for this in one file complete file....
Forum: Bioinformatics 01-27-2014, 09:16 AM
Replies: 5
Views: 1,316
Posted By Nino
No it is not a Sam file. A fastq file consists of...

No it is not a Sam file. A fastq file consists of a header from the machine it was sequence include genomic coordinates plus other information, second line consists of the read itself, third line...
Forum: Bioinformatics 01-27-2014, 07:21 AM
Replies: 5
Views: 1,316
Posted By Nino
Missing header Fastq file

Hello,

I have a fastq file that is missing the header information for 70% of the reads. It is usually the information that starts with an @ and gives the sequencer id plus genomic coordinates....
Forum: Bioinformatics 12-12-2013, 07:38 AM
Replies: 4
Views: 2,276
Posted By Nino
Hey thanks m_two I will look into it.

Hey thanks m_two I will look into it.
Forum: Bioinformatics 12-11-2013, 08:55 AM
Replies: 4
Views: 2,276
Posted By Nino
Yea sorry I do mean just SNPs I guess since the...

Yea sorry I do mean just SNPs I guess since the SNP is on the read and if the read is strand bias then you would filter out that SNP hence the read itself as well.
Forum: Bioinformatics 12-11-2013, 08:53 AM
Replies: 147
Views: 53,457
Posted By Nino
I have sent you an email please look out for a...

I have sent you an email please look out for a med.cornell.edu email.

Thanks,
Nino
Forum: Bioinformatics 12-11-2013, 08:19 AM
Replies: 147
Views: 53,457
Posted By Nino
Pindel version 0.2.5a2, September 17 2013.

Pindel version 0.2.5a2, September 17 2013.
Forum: Bioinformatics 12-11-2013, 08:15 AM
Replies: 4
Views: 2,276
Posted By Nino
Strand bias reads

Hello All,

I would like to know if there is a way to filter out reads that are strand bias. When you upload a bam file to IGV you can see which strand position + or - the read is on and I would...
Forum: Bioinformatics 12-11-2013, 08:07 AM
Replies: 147
Views: 53,457
Posted By Nino
Hello Kaiye, I am running pindel on DNAseq...

Hello Kaiye,

I am running pindel on DNAseq whole exomes data from BWA output and out of the four samples I have one of them gives me segmentation fault. The other three run fine without any issues...
Forum: Bioinformatics 09-24-2013, 06:45 AM
Replies: 218
Views: 133,318
Posted By Nino
Hey Devon, Its turns it is not difficult...

Hey Devon,

Its turns it is not difficult since a group of individual from Case Western Reserve University, Cleveland, OH published a paper on a program they developed called LoQuM which does...
Forum: Bioinformatics 09-19-2013, 07:38 AM
Replies: 218
Views: 133,318
Posted By Nino
Hello I am happy with STAR but not too happy...

Hello

I am happy with STAR but not too happy with the MQ scores it is difficult to filter out reads based on their mapping quality score when you only have 255,3,2,1,0 (I believe 0 is one of them...
Forum: Bioinformatics 06-12-2013, 06:08 AM
Replies: 218
Views: 133,318
Posted By Nino
Hey Nicolas, Star doesnt actually have a...

Hey Nicolas,

Star doesnt actually have a mapping quality score for the reads theirs is setup like this:

255 = uniquely mapped reads
3 = read maps to 2 locations
2 = read maps to 3 locations...
Forum: Bioinformatics 06-10-2013, 09:30 AM
Replies: 20
Views: 13,071
Posted By Nino
Hey Alexdobin, Thanks for the info and help...

Hey Alexdobin,

Thanks for the info and help I was able to get it to work. Cheers!

Nino
Forum: Bioinformatics 06-06-2013, 07:04 AM
Replies: 20
Views: 13,071
Posted By Nino
Star with cufflinks

Hey Guys,

I was wondering if anyone knows how to integrate cufflinks with star. Up until now I have star just for the alignments with chimeric searches, now I need to use cufflinks since searches...
Forum: Bioinformatics 05-20-2013, 09:45 AM
Replies: 1
Views: 1,170
Posted By Nino
Hey, At least yours ejects, mine runs...

Hey,

At least yours ejects, mine runs through without an error in two minutes and processes 0 reads with an empty list in my recal.grp. I have been trying to trouble shoot that even now. Your...
Forum: Bioinformatics 05-20-2013, 08:56 AM
Replies: 0
Views: 669
Posted By Nino
Creating a vcf for one gene from scatch

Hello,

I was tasked to create a vcf file on the SPOP gene from scratch. Two problem:

1.) How do I do it?

2.) Where do I get the variance information from? i.e. reference and alternate allele...
Forum: Bioinformatics 05-20-2013, 08:24 AM
Replies: 5
Views: 1,663
Posted By Nino
I seem to have trouble posting a new thread so...

I seem to have trouble posting a new thread so since this the most relevant place for me to post my question. I am trying to create a vcf file (obviously in vcf format) of the spop gene in human from...
Showing results 1 to 25 of 27

 


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