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Forum: Bioinformatics 09-04-2018, 06:33 AM
Replies: 2
Views: 1,300
Posted By mstagliamonte
Hi, Vivek, Thank you for your answer. Can...

Hi, Vivek,

Thank you for your answer. Can you elaborate on that a bit, please?

Thank you,
Max
Forum: Bioinformatics 08-31-2018, 08:50 AM
Replies: 2
Views: 1,300
Posted By mstagliamonte
Need help with Plink map file

Hi,

I plan to phase my non-human organism genomic data using Shapeit2. I have recombination data available from literature, but I am struggling to understand how to set up the map file. I have...
Forum: Bioinformatics 07-19-2016, 01:53 PM
Replies: 4
Views: 2,386
Posted By mstagliamonte
OK, Thank you for your help

OK,

Thank you for your help
Forum: Bioinformatics 07-19-2016, 10:13 AM
Replies: 4
Views: 2,386
Posted By mstagliamonte
Thank you, Westerman, That's something I...

Thank you, Westerman,

That's something I didn't think of. So basically, the missing bases support an allele that was not called, am I correct?
Forum: Bioinformatics 07-19-2016, 08:47 AM
Replies: 4
Views: 2,386
Posted By mstagliamonte
yet another question regarding vcf format

OK, I am sorry to ask yet another question regarding vcf format, I have noticed there are similar questions asked everywhere, on any forum. Still, I have a doubt, and wonder if I am misunderstanding...
Forum: Bioinformatics 06-02-2016, 11:46 AM
Replies: 6
Views: 1,283
Posted By mstagliamonte
Great, thank you. These sequences are about 0.1%...

Great, thank you. These sequences are about 0.1% of my data, they all seem to have the adapter at the beginning. I'll verify that they are dropped from my dataset when I trim it.

Edit: GenoMax: I...
Forum: Bioinformatics 06-02-2016, 11:14 AM
Replies: 6
Views: 1,283
Posted By mstagliamonte
Thank you, Brian_Bushnell, this makes sense. I am...

Thank you, Brian_Bushnell, this makes sense. I am trying to get a deeper understanding of what I am doing, rather than using the programs as black boxes.
So, basically, if I want to trim the adapter...
Forum: Bioinformatics 06-02-2016, 10:41 AM
Replies: 6
Views: 1,283
Posted By mstagliamonte
Thank you, GenoMax. I just downloaded BBMap; the...

Thank you, GenoMax. I just downloaded BBMap; the adapters.fa has actually the adapters with the individual indexes attached. I will use it on my data.

I am still puzzled regarding the adapter...
Forum: Bioinformatics 06-02-2016, 07:46 AM
Replies: 6
Views: 1,283
Posted By mstagliamonte
Need some clarification regarding adapter trimming

Dear Bioinformaticians,

I'm sorry to admit that after so many posts I've seen regarding the topic, I still have some doubts on how to do it correctly.

I have sequenced (using Illumina Miseq)...
Forum: Bioinformatics 04-13-2016, 09:52 AM
Replies: 2
Views: 3,755
Posted By mstagliamonte
Thank you, I did not realize it would check for...

Thank you, I did not realize it would check for names, thought it would just bluntly take the order of the reads.
The reads have a bit of an uncommon name, being:

read1.1 1
read1.2 1
read2.1 2...
Forum: Bioinformatics 04-13-2016, 06:35 AM
Replies: 2
Views: 3,755
Posted By mstagliamonte
BWA mem on interlaced fastq

Hi, everybody,

I am trying to use bwa mem (v. 0.7.12) on some interleaved fastq files, i.e. the reads are paired end, but they are in one file (the ith read is forward; ith+1 is the reverse).
...
Forum: Bioinformatics 11-04-2015, 11:01 AM
Replies: 2
Views: 3,760
Posted By mstagliamonte
Thanks! I realize now it was a bit of a naive...

Thanks! I realize now it was a bit of a naive question, I'll do it straight away :)

Best,
Max
Forum: Bioinformatics 11-03-2015, 02:42 PM
Replies: 2
Views: 3,760
Posted By mstagliamonte
TABIX on generic tab file

Hi, Everybody,

I have a 1-based, tab-delimited file with some annotations, which I would like to use with bcftools annotate on a vcf file.
The fields are:
CHROM, START, END, FEATURE, and a...
Forum: Bioinformatics 07-23-2014, 02:34 PM
Replies: 2
Views: 1,131
Posted By mstagliamonte
Thanks, I'll try :) Regards, Max

Thanks, I'll try :)

Regards,
Max
Forum: Bioinformatics 07-23-2014, 08:19 AM
Replies: 2
Views: 1,131
Posted By mstagliamonte
Samtools and intrasample diversity

Hi, Seqanswers community,

I need some help with my variant calling.

I am dealing with a monocellular organisms, and I am expecting intrasample diversity due to multiclonality. This could mean...
Forum: Bioinformatics 03-27-2014, 03:30 PM
Replies: 0
Views: 1,041
Posted By mstagliamonte
Genome Mappability Analyzer

Hi, Everybody,

Has anyone ever used Genome Mappability Analyzer (http://www.ncbi.nlm.nih.gov/pubmed/?term=genome+mappability+analyzer)? It seems very appealing to me, but I am having some problems...
Forum: Bioinformatics 01-03-2014, 06:47 AM
Replies: 2
Views: 1,625
Posted By mstagliamonte
... Thanks. I do not remember on which computer I...

... Thanks. I do not remember on which computer I originally stored the files. I am going to download them again and try. Hope that is the problem.

Regards,
Max
Forum: Bioinformatics 01-03-2014, 06:10 AM
Replies: 2
Views: 1,625
Posted By mstagliamonte
Trying to convert embl to fasta: problems with Emboss 6.5.7

Hi, everyone,

and Happy New Year.

I am trying to convert some embl files to fasta using EMBOSS 6.5.7. The problem is that the resulting files have got a sequence length different from the...
Forum: Bioinformatics 12-18-2013, 01:02 PM
Replies: 0
Views: 1,201
Posted By mstagliamonte
PICARD replace group error

... not yet another read group thread... :rolleyes:

Hi, everybody,

I am trying to set up a GATK analysis. I have two strains of the same microorganism, one MiSeq run (one lane) with one sample...
Forum: Bioinformatics 11-27-2013, 01:01 PM
Replies: 2
Views: 2,005
Posted By mstagliamonte
Hey, Thanks for your suggestion. ...

Hey,

Thanks for your suggestion.

Regards,
Max
Forum: Bioinformatics 11-26-2013, 06:48 AM
Replies: 2
Views: 2,005
Posted By mstagliamonte
Apicomplexa (Plasmodium spp.) SNP analysis - ploidy

Dear All,

I am learning SNP analysis to be carried out on Plasmodium parasites. These parasites have a diploid state in the mosquito, but are then haploid in the human host. This makes me think I...
Forum: Bioinformatics 10-18-2013, 12:45 PM
Replies: 6
Views: 2,263
Posted By mstagliamonte
Hey, Thank you! Found what I was looking...

Hey,

Thank you! Found what I was looking for. Thank goodness!

I was afraid I would have to go out and socialize this weekend. You're a life saver :D

Max
Forum: Bioinformatics 10-18-2013, 08:29 AM
Replies: 6
Views: 2,263
Posted By mstagliamonte
Looking for GATK manual - site down

Hi everyone,

The GATK web site is down for a few days. Has anyone got GATK mauals in pdf or similar formats? I'm just looking for some relaxing reading over the weekend... ;)

Thanks
Max
Forum: Bioinformatics 08-01-2013, 03:02 AM
Replies: 3
Views: 4,274
Posted By mstagliamonte
Thanks, to the both of you :) I know a bit...

Thanks, to the both of you :)

I know a bit of Python, but I wasn't sure why the cat command would not generate valid files. that is really interesting, good to know for the future.
I will review...
Forum: Bioinformatics 07-29-2013, 11:59 PM
Replies: 3
Views: 4,274
Posted By mstagliamonte
Merging Blast results - xml or tabular format

Hi, everybody,

I have broken a large fasta file into smaller ones, and run parallel BLAST queries on multiple processors. I was thinking to merge the output files with cat - but I later realised...
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