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Search: Posts Made By: neha
Forum: Bioinformatics 06-11-2015, 11:27 PM
Replies: 1
Views: 4,962
Posted By neha
Exclamation Error in installing DBD::mysql on ubuntu 14.04

Hi All

I am trying to install DBD::mysql module on ubuntu 14.04. I have installed DBI module using the following command

perl -MCPAN -e 'install DBI' and it installed without any error. I also...
Forum: Bioinformatics 02-13-2014, 01:18 AM
Replies: 1
Views: 1,363
Posted By neha
running Glimmer3.02 on multi-fasta file

Hello everyone,

I have around 2000 bacterial contigs obtained after de novo assembly. I want to annotate them using glimmer. Glimmer takes one contig at a time and predicts gene but I want that it...
Forum: Bioinformatics 10-31-2013, 06:50 AM
Replies: 0
Views: 1,075
Posted By neha
SHRiMP mapping algorithm

Hello everyone,

I have miRNA data generated through ION PGM. I am using SHRiMP software for mapping. I want to know how exactly SHRiMP algorith works

It is written that by default it makes 3...
Forum: SOLiD 06-24-2013, 04:26 AM
Replies: 0
Views: 2,948
Posted By neha
explanation about hard clip and soft clip reads

Hello Everyone,

I am working on SOLiD data. I am using Lifescope v2.5.1 for mapping of reads. SAM file obtained after mapping contains CIGAR string in form of hard clip and soft clip.

I was...
Forum: Bioinformatics 06-06-2013, 04:15 AM
Replies: 4
Views: 9,123
Posted By neha
Thank you so much mbblack for explaining it in...

Thank you so much mbblack for explaining it in such a nice way.
Forum: Bioinformatics 06-05-2013, 02:47 AM
Replies: 4
Views: 9,123
Posted By neha
Mapping quality value

Hello everyone,

I just want to know how important is mapping quality value when we align the next generation sequencing data with any of the software like bowtie, bwa or bfast. I mean if reads...
Forum: General 03-12-2013, 02:47 AM
Replies: 3
Views: 4,958
Posted By neha
Thanks kmcarr and Dario. I will try Picard...

Thanks kmcarr and Dario. I will try Picard utility and hope it will solve my problem.

Thanks,
Neha
Forum: General 03-05-2013, 10:18 PM
Replies: 3
Views: 4,958
Posted By neha
bowtie priduced SAm file does not have RG tags in alignment

Hello Everyone,

I have used bowtie for mapping my reads to human genome. Bowtie directly outputs the SAM file using -S option but then I realized that SAM file produced does not have the RG tags...
Forum: Bioinformatics 01-02-2013, 03:46 AM
Replies: 0
Views: 1,767
Posted By neha
Query regarding contigs order by Mauve contig mover

Hello Everyone,

I have around 300 contigs from a newly sequenced bacterial strain and MCM does four iteration. In fourth iteration it produces a .tab file which contains all information about the...
Forum: Bioinformatics 09-26-2012, 11:21 PM
Replies: 1
Views: 1,134
Posted By neha
Explanation Of bayesian and Frequentist algorithm

Hello Everyone,

can anyone explain me with example how Bayesian and Frequentist algorithm calculates the probability of finding a variant at particular position. I do understand these algorithms...
Forum: Bioinformatics 07-17-2012, 10:49 PM
Replies: 8
Views: 10,741
Posted By neha
Regarding DNAplotter

Hello everyone

I have done re-sequencing of one of Vibrio cholerae strain and has data in form of consensus sequence for both the chromosomes. Now I want to make these consensus circular and...
Forum: Bioinformatics 05-30-2012, 02:56 AM
Replies: 14
Views: 8,893
Posted By neha
Hello Everyone, When using...

Hello Everyone,

When using VariantRecalibrator walker of GATK I am facing a small problem.

I am using the following command

java -jar ./../GenomeAnalysisTK.jar -T VariantRecalibrator -R...
Forum: Bioinformatics 05-28-2012, 01:20 AM
Replies: 22
Views: 4,650
Posted By neha
I got the read counts from Partek software. It...

I got the read counts from Partek software. It does give read count in fraction.
Forum: Bioinformatics 05-25-2012, 05:03 AM
Replies: 22
Views: 4,650
Posted By neha
Difficulty in DESeq

Hello Simon,

I am quite new to R. I am trying to do differential expression analysis for RNA-seq data using DESeq. my original file looks like this:

wildtype mutant
A1BG 6 ...
Forum: Bioinformatics 04-25-2012, 01:27 AM
Replies: 3
Views: 3,914
Posted By neha
Hello everyone, I have exome data from SOLiD...

Hello everyone,

I have exome data from SOLiD 5500. I am doing variant analysis using GATK UnifiedGenotyper module. The parameters I use are

java -jar ./../GenomeAnalysisTK.jar -glm SNP -R...
Forum: Bioinformatics 03-25-2012, 11:24 PM
Replies: 5
Views: 3,639
Posted By neha
Maping quality does not tell whether reads are...

Maping quality does not tell whether reads are uniquely mapped or duplicate. It signifies the hypothesis of having confidence that read mapping to particular genomic position is correct. Higher the...
Forum: RNA Sequencing 03-25-2012, 11:11 PM
Replies: 11
Views: 13,630
Posted By neha
Hi, I want to download all human rRNA genes...

Hi,

I want to download all human rRNA genes and as suggested by you I have gone through this database but the only confusion I have is it does not report whether it is 5.8S rRNA gene sequence or...
Forum: Bioinformatics 03-21-2012, 09:23 PM
Replies: 5
Views: 3,639
Posted By neha
Hi , I think if you want to call variants...

Hi ,

I think if you want to call variants only on uniquely mapped reads you can first remove duplicates using picardtools and then call variants using GATK.

Also you can do per base score...
Forum: Bioinformatics 03-21-2012, 09:17 PM
Replies: 14
Views: 8,893
Posted By neha
Hey did You get the chance to see the files. ...

Hey did You get the chance to see the files.

Any help would be appreciated.

Neha
Forum: Bioinformatics 03-19-2012, 09:57 PM
Replies: 14
Views: 8,893
Posted By neha
I am attaching the doc file for hapmap3.3 and...

I am attaching the doc file for hapmap3.3 and 1000_genome_file. By seeing Hapmap3.3 file I am guessing there is something wrong with this file or may be I am confused this file looks like this only....
Forum: Bioinformatics 03-19-2012, 06:07 AM
Replies: 14
Views: 8,893
Posted By neha
Problem in running VariantRecalibrator

Hello Everyone,

I am trying to run the GATK variantRecalibrator but getting an error message.
command I am using to run it is


java -jar GenomeAnalysisTK.jar -R results/test_human.fasta -T...
Forum: Bioinformatics 03-14-2012, 07:16 AM
Replies: 14
Views: 5,416
Posted By neha
Thank you so much. I dont know why I was doing...

Thank you so much. I dont know why I was doing the blunder of typing KnownSites instead of "knownSites". Now it is running perfectly fine.

My UnifiedGenotyper module is also running perfectly...
Forum: Bioinformatics 03-14-2012, 03:04 AM
Replies: 13
Views: 4,286
Posted By neha
You can download the GRCh37 files from UCSC...

You can download the GRCh37 files from UCSC browser or Broad institute ftp sites.
Forum: Bioinformatics 03-06-2012, 08:42 PM
Replies: 14
Views: 5,416
Posted By neha
Hey sorry for that error message. By mistake I...

Hey sorry for that error message. By mistake I ran the wrong command but even after correcting it to --KnownSites I am getting the same error.

##### ERROR
##### ERROR MESSAGE: Argument with name...
Forum: Bioinformatics 03-05-2012, 12:34 AM
Replies: 14
Views: 5,416
Posted By neha
I am getting this error for CountCovariate ...

I am getting this error for CountCovariate
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version...
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