Forum: Bioinformatics
09-17-2019, 02:06 PM
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Replies: 0
Views: 1,476
Script to calculate Dipeptide composition
Hi all, I would like to use a script (python, shell, or perl) to calculate the percentages of dipeptide composition from multiple protein sequences (fasta format). Any suggestion?
I do not want to...
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Forum: Bioinformatics
10-16-2018, 12:53 PM
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Replies: 0
Views: 997
Remove duplicate genes/mRNA from a gff file
I would like to combine two different gff files and then remove some duplicate genes/mRNA/exons with overlaps. I did not find any tool to do it. There is an option using bedtools to merge two gff...
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Forum: Bioinformatics
09-21-2017, 07:04 AM
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Replies: 7
Views: 5,270
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...
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Forum: Bioinformatics
09-08-2017, 02:10 PM
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Replies: 4
Views: 2,556
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Forum: Bioinformatics
09-08-2017, 08:54 AM
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Replies: 4
Views: 2,556
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...
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Forum: Bioinformatics
09-07-2017, 03:12 PM
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Replies: 7
Views: 5,270
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Forum: Bioinformatics
02-09-2017, 01:47 PM
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Replies: 7
Views: 6,144
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...
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Forum: Bioinformatics
02-08-2017, 11:57 AM
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Replies: 7
Views: 6,144
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...
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Forum: Bioinformatics
02-02-2017, 11:33 AM
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Replies: 0
Views: 3,051
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...
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Forum: Bioinformatics
02-01-2017, 01:21 PM
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Replies: 3
Views: 2,220
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...
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Forum: Bioinformatics
02-01-2017, 09:22 AM
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Replies: 3
Views: 2,220
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).
...
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Forum: Bioinformatics
01-30-2017, 08:01 AM
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Replies: 3
Views: 3,399
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Forum: Bioinformatics
01-26-2017, 10:56 AM
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Replies: 3
Views: 3,399
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...
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Forum: Bioinformatics
06-02-2016, 10:54 AM
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Replies: 3
Views: 4,560
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...
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Forum: Bioinformatics
06-01-2016, 06:10 AM
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Replies: 3
Views: 4,560
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...
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Forum: RNA Sequencing
03-23-2016, 02:42 PM
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Replies: 0
Views: 1,070
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...
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Forum: Bioinformatics
03-08-2016, 09:59 AM
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Replies: 19
Views: 9,780
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...
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Forum: Literature Watch
10-20-2015, 10:30 AM
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Replies: 46
Views: 42,090
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Forum: Bioinformatics
09-30-2015, 11:46 AM
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Replies: 1
Views: 1,412
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...
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Forum: Bioinformatics
05-13-2015, 09:54 AM
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Replies: 1
Views: 1,267
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...
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Forum: Bioinformatics
05-13-2015, 09:49 AM
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Replies: 2
Views: 3,306
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Forum: Bioinformatics
03-31-2015, 07:39 AM
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Replies: 0
Views: 1,138
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...
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Forum: Bioinformatics
03-03-2015, 04:15 AM
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Replies: 4
Views: 2,591
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...
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Forum: Bioinformatics
03-02-2015, 11:19 AM
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Replies: 4
Views: 2,591
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Forum: Bioinformatics
03-02-2015, 05:14 AM
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Replies: 4
Views: 2,591
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