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Search: Posts Made By: clarissaboschi
Forum: Bioinformatics 09-21-2017, 06:04 AM
Replies: 7
Views: 1,548
Posted By clarissaboschi
Thanks for the suggestions. I have a list of...

Thanks for the suggestions.
I have a list of protein ids, and I need to retrieve the respective nucleotide sequence. I am using eutils to retrieve them based on these ids, but for some ids, I have...
Forum: Bioinformatics 09-08-2017, 01:10 PM
Replies: 4
Views: 773
Posted By clarissaboschi
GenoMax, I tried to use -num_alignments 5 and did...

GenoMax, I tried to use -num_alignments 5 and did not work...I got many hits.
Forum: Bioinformatics 09-08-2017, 07:54 AM
Replies: 4
Views: 773
Posted By clarissaboschi
How to output 5 top hits using standalone blast

I am using blast, and I would like to filter my results, not based on the best hit, but the top 5 hits.

I do not want to use the option "-max_target_seqs" because it does not result in the correct...
Forum: Bioinformatics 09-07-2017, 02:12 PM
Replies: 7
Views: 1,548
Posted By clarissaboschi
How to extract the longest sequence from a fasta file

I have a fasta file with many sequences, an I would like to get just the longest one (does not matter the id). How can I do that?

I would like to have as output a fasta file with only the longest...
Forum: Bioinformatics 02-09-2017, 12:47 PM
Replies: 7
Views: 4,341
Posted By clarissaboschi
Thanks tomc for your detailed explanation and...

Thanks tomc for your detailed explanation and time to answer it.

This was exactly what I did. I wrote a shell script in different steps. I was not able to write a python script because I am...
Forum: Bioinformatics 02-08-2017, 10:57 AM
Replies: 7
Views: 4,341
Posted By clarissaboschi
And how can I do this comparison? I mean I...

And how can I do this comparison?

I mean I already have the output results from blast (axb and bxa). So how can I compare them and get the matches between the 2 files?

Should I use unix...
Forum: Bioinformatics 02-02-2017, 10:33 AM
Replies: 0
Views: 1,105
Posted By clarissaboschi
Megablast x dc-megablast

When I should use discontinuous Megablast instead of Megablast? I do not know which blast is better to use for nucleotide blast.

I read some information about it as follow:

Megablast: Retrieves...
Forum: Bioinformatics 02-01-2017, 12:21 PM
Replies: 3
Views: 996
Posted By clarissaboschi
maubp it is a good paper, but did not help me,...

maubp it is a good paper, but did not help me, because is more focus in protein sequence analysis. I know is better to use protein sequences for it, but I need to use nucleotide sequences.

I am...
Forum: Bioinformatics 02-01-2017, 08:22 AM
Replies: 3
Views: 996
Posted By clarissaboschi
Blastn x megablast - homologous genes

I have a list of nucleotide sequences (genes) and I would like to Blast against a list of nucleotide sequences from other species to check potential homologous sequences (orthologs and paralogs).
...
Forum: Bioinformatics 01-30-2017, 07:01 AM
Replies: 3
Views: 1,418
Posted By clarissaboschi
Ok, thanks I will check it. I tried by using bed...

Ok, thanks I will check it. I tried by using bed file format and it worked very well.
Forum: Bioinformatics 01-26-2017, 09:56 AM
Replies: 3
Views: 1,418
Posted By clarissaboschi
CrossMap analysis

I am trying to convert some genome coordinates of SNPs in one vcf file using the CrossMap program (http://crossmap.sourceforge.net/).

I am having difficulties with the conversion. My vcf file does...
Forum: Bioinformatics 06-02-2016, 09:54 AM
Replies: 3
Views: 2,352
Posted By clarissaboschi
Thanks Colindaven, yes I was thinking that the...

Thanks Colindaven, yes I was thinking that the issue is on my QTL file that I got from a database.
I already found different issues in this file, like start position bigger than end position and...
Forum: Bioinformatics 06-01-2016, 05:10 AM
Replies: 3
Views: 2,352
Posted By clarissaboschi
QTL overlap (bedtools)

Dear all, I am trying to compare some QTL regions with specific genome regions that I have, for it I am using bedtools.
I used before bedtools with a list of genes and it worked well, but this time...
Forum: RNA Sequencing 03-23-2016, 01:42 PM
Replies: 0
Views: 782
Posted By clarissaboschi
Smile number of reads for sQTL detection

Dear all,

I would like to know the recommendation of number of reads (coverage) for the splice QTL detection (from RNA seq data).

Here...
Forum: Bioinformatics 03-08-2016, 08:59 AM
Replies: 19
Views: 6,643
Posted By clarissaboschi
I have a doubt about Fst from VCFtools....

I have a doubt about Fst from VCFtools. :confused:

I used VCFtools to obtain Fst, but VCFtools generates 2 different Fst: mean and weighted.

Which one is best to consider? In my cases these 2...
Forum: Literature Watch 10-20-2015, 09:30 AM
Replies: 46
Views: 32,029
Posted By clarissaboschi
Alicia, I gave up to use CNV-seq tool and I am...

Alicia, I gave up to use CNV-seq tool and I am using CNVnator which I do not need any reference.
Forum: Bioinformatics 09-30-2015, 10:46 AM
Replies: 1
Views: 948
Posted By clarissaboschi
Genotypes conversion (SNP chip)

Hi all,
I have a big input file from 28 individuals which were genotyped by 600 K SNP chip (Affymetrix). I have about ~500,000 genotypes for each individual.
But my file has a particular format for...
Forum: Bioinformatics 05-13-2015, 08:54 AM
Replies: 1
Views: 783
Posted By clarissaboschi
CNV annotation tool

Dear all,

I detected CNVs with CNVnator tool from seq-data and after I identified the CNV regions with CNVruler. Now I need to annotate these regions.

Which tool I can use for it? I know that...
Forum: Bioinformatics 05-13-2015, 08:49 AM
Replies: 2
Views: 1,873
Posted By clarissaboschi
I think CNVnator is a good tool for it.

I think CNVnator is a good tool for it.
Forum: Bioinformatics 03-31-2015, 06:39 AM
Replies: 0
Views: 819
Posted By clarissaboschi
Codon Adaptation Index (CAI) for chicken

Dear members

I am trying to get the Codon Adaptation Index for few genes, but the online tools that I have tried there is no chicken genome option.
Some tools are old and I was not able to...
Forum: Bioinformatics 03-03-2015, 03:15 AM
Replies: 4
Views: 1,701
Posted By clarissaboschi
Thanks lindenb, I will try your script Your...

Thanks lindenb, I will try your script

Your script does maintain the header of the vcf? Because I need.

Actually I want the alternative allele (SNP allele), but sometimes there are different...
Forum: Bioinformatics 03-02-2015, 10:19 AM
Replies: 4
Views: 1,701
Posted By clarissaboschi
Thanks sarvidsson I saw this option. In my...

Thanks sarvidsson

I saw this option. In my case I think the one that I need is:

#Only loci with enough reads supporting the variant will pass the filter
{
tag => 'INFO/DP4',
...
Forum: Bioinformatics 03-02-2015, 04:14 AM
Replies: 4
Views: 1,701
Posted By clarissaboschi
vcf file - filter based on DP4 (not total) and removal alternative alleles

Hi all,

I'm using samtools/mpileup to find variants in my resequencing data of multiple samples together. I and got one vcf file with SNPs and Indels.
I am applying many different filtrations but...
Forum: Bioinformatics 02-25-2015, 04:54 AM
Replies: 2
Views: 1,240
Posted By clarissaboschi
I used samtools/mpileup and different filter...

I used samtools/mpileup and different filter parameters.
I am wondering if it is a good idea to use SNP cluster as a filter as well

Example remove snps when- 3 SNPs/10 bases as suggested in the...
Forum: Bioinformatics 02-24-2015, 10:12 AM
Replies: 7
Views: 1,770
Posted By clarissaboschi
Dear aforntacc I know that this post is old,...

Dear aforntacc

I know that this post is old, but reading about the filters that you used for filter the variants I noticed that you have one particular filter called "AltSup" that I am interested....
Showing results 1 to 25 of 61

 


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