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Search: Posts Made By: m_elena_bioinfo
Forum: Bioinformatics 03-23-2016, 02:06 AM
Replies: 1
Views: 4,320
Posted By m_elena_bioinfo
Calculate uniformity of coverage

Dear all,
How can I calculate the uniformity of coverage (% of bases >0.2x mean)from a bam file?
Thanks!!
Forum: Bioinformatics 07-04-2014, 02:09 AM
Replies: 0
Views: 754
Posted By m_elena_bioinfo
denovogear parameter

I'm trying to use denovogear to extract de novo variants from exome trios. Anyone can explain me the difference in the output parameter?
tgt_null/tgt_dnm
pp_null/pp_dnm
What parameter I have to...
Forum: Bioinformatics 09-25-2013, 04:13 AM
Replies: 1
Views: 1,366
Posted By m_elena_bioinfo
ngsrich error coverage

Dear, i'm computing the coverage of a whole exome.
I run NGSrich as:

> java NGSrich evaluate -r file.bam.sorted.bam -u hg19 -a refGene.txt -t designwes.bed -o outputdir -s name

and the...
Forum: Bioinformatics 07-08-2013, 08:38 AM
Replies: 9
Views: 6,893
Posted By m_elena_bioinfo
analysis amplicon miseq

Dear,
I sequenced 5 genes using truseq custom amplicon kit on Miseq. But if I process the data using bwa + samtools, the results seem to be not good.
Anyone has any idea about the pipeline of...
Forum: Bioinformatics 07-08-2013, 07:44 AM
Replies: 13
Views: 10,239
Posted By m_elena_bioinfo
the problem is the index of genome.fasta if I...

the problem is the index of genome.fasta
if I use bwa0.6.2 for sampe, it returns me:

[bns_restore_core] fail to open file '/dati1/reference/genomes/hg19.fasta.nt.ann'. Abort!

i have tried to...
Forum: Bioinformatics 07-08-2013, 05:08 AM
Replies: 13
Views: 10,239
Posted By m_elena_bioinfo
bwa sampe error

Dear,
I run BWA 0.7.5a
>bwa aln genome.fasta read1.fastq > read1.sai
>bwa aln genome.fasta read2.fastq > read2.sai
> bwa sampe -r '@RG\tID:s\tLB:ss\tPL:ILLUMINA\tPU:l1\tSM:' genome.fasta...
Forum: Bioinformatics 04-23-2013, 01:41 AM
Replies: 2
Views: 1,258
Posted By m_elena_bioinfo
I use bwa, samtools rmdup to remove duplicates...

I use bwa, samtools rmdup to remove duplicates (not -S option), gatk for local realignment and recalibration.
The reads before alignment are trimmed randomly. In the figure you can see three reads...
Forum: Bioinformatics 04-23-2013, 12:29 AM
Replies: 2
Views: 1,258
Posted By m_elena_bioinfo
problem with R2 reads from Miseq

Dear, I have a problem in Miseq data. I have paired 2x150bp reads. I have identified some false positive (repetitive in different samples) due to short mapped reads. In fastq files (both R1 and R2) I...
Forum: Bioinformatics 03-11-2013, 11:43 PM
Replies: 2
Views: 1,069
Posted By m_elena_bioinfo
read different length in fastq

Dear,
I have performed two runs (targeted sequencing) on miseq using 2x150bp protocol. Unusually, I have obtained fastq containing reads of different length, that during alignment step cause...
Forum: Sample Prep / Library Generation 02-01-2013, 06:08 AM
Replies: 0
Views: 1,115
Posted By m_elena_bioinfo
enrichment efficiency

Dear,
I have design two different panels for two different diseases. The dimension of the target regions are the same (about 1.9Mb), in the first I there are 100 genes (only the exons), while in the...
Forum: Bioinformatics 01-28-2013, 07:43 AM
Replies: 4
Views: 6,601
Posted By m_elena_bioinfo
Thank you very much for your help! The program...

Thank you very much for your help! The program runs and I have generated the new fastq. The last question is: how can I know from MISEQ reporter when the requeue and the rerun of "data extraction"...
Forum: Bioinformatics 01-28-2013, 05:45 AM
Replies: 4
Views: 6,601
Posted By m_elena_bioinfo
GReat! You are right! I fix my problem, I have...

GReat! You are right! I fix my problem, I have wrong the index sequences in the sample sheet. So now, I have to re-demultiplex the sequences with the right indexes. How can I do this?
Forum: Bioinformatics 01-28-2013, 04:21 AM
Replies: 4
Views: 6,601
Posted By m_elena_bioinfo
miseq undetermined fastq

Good morning, I have a problem with miseq run.
I have generated 500Mb of Undetermined_sequence.fastq.gz and a sample in the trio was empty.
How can I determine raw index sequences in Undetermined...
Forum: Bioinformatics 07-24-2012, 11:11 PM
Replies: 1
Views: 1,055
Posted By m_elena_bioinfo
CASAVA library problem

Dear,
the installation of CASAVA1.8 with cmake is not trivial for me!
I download the tar file, and tried to install all by cmake. But I have a problem in define library @CASAVA_FULL_PERL_LIBDIR@...
Forum: Bioinformatics 05-31-2012, 04:54 AM
Replies: 5
Views: 3,951
Posted By m_elena_bioinfo
Hi! I've the same problem: known deletion and...

Hi!
I've the same problem: known deletion and SNP in a sample that I can't detected by variant calling in RNASeq alignment from Tophat.
Have you fix the problem?
Thanx a lot
Forum: Bioinformatics 04-11-2012, 05:08 AM
Replies: 3
Views: 5,052
Posted By m_elena_bioinfo
Thanks a lot, now the program runs!!! The...

Thanks a lot, now the program runs!!!
The tutorial is not so user-friendly for me (i'm beginner in R)...anyone can help me?
Forum: Bioinformatics 04-11-2012, 01:23 AM
Replies: 3
Views: 5,052
Posted By m_elena_bioinfo
cummeRbund installation

Hi,
I'm trying to install cummeRbund package for final analysis of cufflinks outputs.
In R,
>install.packages("cummeRbund", dependencies = TRUE)
the error is that
package 'cummeRbund' is not...
Forum: Bioinformatics 04-10-2012, 11:24 PM
Replies: 1
Views: 884
Posted By m_elena_bioinfo
RNASeq

Dear,
anyone could help me to "understand" the outputs of cufflinks?
How can I use these data and FPKM values to extract the differential gene expression and the different abundance of isoforms?
...
Forum: Bioinformatics 04-06-2012, 06:58 AM
Replies: 34
Views: 9,451
Posted By m_elena_bioinfo
CONTRA cnv targeted resequencing

Dear I'm trying to run CONTRA on my data (targeted resequencing) to detect CNV in exons. The program returns me this error:

Traceback (most recent call last):
File "contra.py", line 34, in...
Forum: Bioinformatics 03-14-2012, 02:58 AM
Replies: 14
Views: 5,115
Posted By m_elena_bioinfo
try --knownSites and not --KnownSites

try --knownSites and not --KnownSites
Forum: Bioinformatics 03-14-2012, 02:30 AM
Replies: 3
Views: 1,207
Posted By m_elena_bioinfo
Thank you Nancy, you are right! I was using the...

Thank you Nancy, you are right! I was using the wrong reference fasta file. Now bam2mpg run correctly and your explanation about the column data are very useful for me!
Forum: Bioinformatics 03-07-2012, 01:34 AM
Replies: 14
Views: 5,115
Posted By m_elena_bioinfo
Please, post me how you run the program!

Please, post me how you run the program!
Forum: Bioinformatics 03-05-2012, 12:38 AM
Replies: 14
Views: 5,115
Posted By m_elena_bioinfo
The program return:ERROR MESSAGE: Argument with...

The program return:ERROR MESSAGE: Argument with name 'KnowbSites' isn't defined.

But it is not "knowbsites", but knownSites, with the same uppercase letters!
Forum: Bioinformatics 03-01-2012, 04:01 AM
Replies: 14
Views: 5,115
Posted By m_elena_bioinfo
Maybe the format of your dbsnp.vcf is the...

Maybe the format of your dbsnp.vcf is the problem. Can you post your error message?
Forum: Bioinformatics 02-27-2012, 05:40 AM
Replies: 14
Views: 5,115
Posted By m_elena_bioinfo
Dear Neha, I run GATK to recalibrate score as:...

Dear Neha, I run GATK to recalibrate score as: (i'm using version 1.3-25-g32cdef9) (this way it's ok)

> java -jar GenomeAnalysisTK.jar -R hg19.fasta -I sample.bam.sorted.bam --knownSites:dbsnp,VCF...
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