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Forum: De novo discovery 01-12-2016, 05:15 AM
Replies: 38
Views: 15,031
Posted By arthurmelo
Hi everybody, I wondering to introduce and share...

Hi everybody, I wondering to introduce and share the GBS-SNP-CROP:a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-...
Forum: Bioinformatics 01-12-2016, 04:51 AM
Replies: 1
Views: 1,386
Posted By arthurmelo
GBS-SNP-CROP: a reference-optional pipeline for SNP discovery

Hi everybody, I wondering introduce and share the GBS-SNP-CROP: a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping-by-...
Forum: RNA Sequencing 12-21-2015, 08:25 AM
Replies: 8
Views: 4,387
Posted By arthurmelo
Hi, assuming you first parsed your data based on...

Hi, assuming you first parsed your data based on quality analysis using a Phred score Q>20, you certain could set the minimum length for acceptable contigs to 500 bp, for example, using...
Forum: MGISEQ (FKA Complete Genomics) 12-13-2015, 10:14 AM
Replies: 3
Views: 5,344
Posted By arthurmelo
Normally all reads has the same length on raw...

Normally all reads has the same length on raw sequenced data. It explain the equal values of min and max read length. Generally the raw dataset is parsed by some bioinformatic tool like trimmomatic...
Forum: Bioinformatics 07-02-2015, 06:22 PM
Replies: 3
Views: 1,089
Posted By arthurmelo
Hi Rhewter.. I hope you are well... The main...

Hi Rhewter.. I hope you are well...
The main question before try to help you is understand what SNP do you want to keep. Probably you need to choice some SNP trait like depth or allele frequence and...
Forum: Bioinformatics 03-04-2015, 05:15 AM
Replies: 3
Views: 2,854
Posted By arthurmelo
look this examples in vcftools ... ...

look this examples in vcftools ...
http://vcftools.sourceforge.net/perl_examples.html
Forum: Bioinformatics 02-09-2015, 06:37 AM
Replies: 4
Views: 3,754
Posted By arthurmelo
I think it's necessary to use the -know option of...

I think it's necessary to use the -know option of RealignerTargetCreator. My first attempt to fix this problem was use --fix_misencoded_quality_scores GATK option, but it' not possible. When I use a...
Forum: Bioinformatics 11-21-2014, 04:03 AM
Replies: 7
Views: 2,158
Posted By arthurmelo
Hello trotos, I think I can fix the problem...

Hello trotos,
I think I can fix the problem determining a limit for Java memory, with "MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=" option. I'm using the follow script

java -jar...
Forum: Bioinformatics 10-13-2014, 06:21 AM
Replies: 7
Views: 2,158
Posted By arthurmelo
OK Devon Ryan, So sorry. But do you know...

OK Devon Ryan, So sorry.
But do you know anything about my question?
Forum: Bioinformatics 10-13-2014, 04:33 AM
Replies: 7
Views: 2,158
Posted By arthurmelo
Picard MarkDuplicates VM warning: fix the library

Dears, I'm running Picard to MarkDuplicates in a _merged.sorted.bam file from RNA-seq data. My script is:

java -Xmx5g -jar /usr/local/picard-tools-1.119/MarkDuplicates.jar INPUT=merged.sorted.bam...
Forum: Illumina/Solexa 07-16-2014, 10:58 AM
Replies: 18
Views: 7,965
Posted By arthurmelo
Hello people, I have any problem with Masurca...

Hello people,
I have any problem with Masurca assembler. I think that problem is in Jellyfish step.
The error is related with close gaps: "Gap close failed, you can still use pre-gap close files...
Forum: Bioinformatics 04-09-2014, 04:52 AM
Replies: 12
Views: 6,115
Posted By arthurmelo
Thank you so much rkizen.

Thank you so much rkizen.
Forum: Bioinformatics 04-09-2014, 03:59 AM
Replies: 12
Views: 6,115
Posted By arthurmelo
Hi everbody ... change the discussion focus,...

Hi everbody ...
change the discussion focus, how is the real mean of -C (Cutoff) option in normalize-by-median.py script. The Digital Normalization authors suggested -C 20. But I don't sure if only...
Forum: Bioinformatics 03-25-2014, 06:33 AM
Replies: 3
Views: 5,282
Posted By arthurmelo
I think this command is good ... samtools...

I think this command is good ...
samtools mpileup -uD -f <reference>.fasta ./1_sorted.bam ./2_sorted.bam ./3_sorted.bam ./4_sorted.bam | bcftools view -bvcg - > SNPs.raw.bcf
bcftools view...
Forum: Bioinformatics 05-10-2013, 08:32 AM
Replies: 1
Views: 1,391
Posted By arthurmelo
KmerGenie output

Hi folks...

I use KmerGenie to determinate the best Kmer number in bruijn graphs construction, but resut was : " could not fit histograms ..."

I use script ./kmergenie reads_file

Somebody...
Forum: Bioinformatics 05-10-2013, 08:19 AM
Replies: 2
Views: 2,044
Posted By arthurmelo
Use DNASP software to estimate parameters of...

Use DNASP software to estimate parameters of neutrality test. This software is more easy than arlequin.
If you want to use arlequin, I sugested that you create your input file using CREATE software....
Forum: Literature Watch 09-25-2012, 09:19 AM
Replies: 3
Views: 3,008
Posted By arthurmelo
Hi protist, wanderfull and recent work. It`s...

Hi protist, wanderfull and recent work.
It`s very interesting the SEQanswers people share good publication/papers in NGS approach.

Thanks
Forum: Literature Watch 09-25-2012, 03:53 AM
Replies: 3
Views: 3,008
Posted By arthurmelo
See this paper too: Differential gene and...

See this paper too:

Differential gene and transcript expression analysis of RNA-Seq experiments with TopHat and Cufflinks.

Trapnell et al. (2012) Nature protocols, 7:562-578
Forum: Introductions 07-03-2012, 06:54 AM
Replies: 0
Views: 669
Posted By arthurmelo
Hello NGS and bioinformatic community

Hello people.. I'm Arthur Melo a brazilian PhD studant in Genetic and Plant Breeding in Federal University of Goias State. In our plant genomic Lab we research group work with high throughput...
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