User: daniel.silvestre

Reputation:
70
Status:
New User
Location:
Brazil
Last seen:
4 years, 3 months ago
Joined:
5 years, 1 month ago
Email:
d***************@hc.fm.usp.br

Posts by daniel.silvestre

<prev • 10 results • page 1 of 1 • next >
0
votes
1
answer
615
views
1
answers
Comment: C: Failed assertion in subjunc aligner for large indels
... Thanks for the explanations. I'll adjust my parameters. We're interested in small indels at this moment. But, all my samples (cases and controls) seem to possess long indels. About threads, after some testing, I've sticked to 16 threads per sample, with four samples per node running at the same time ...
written 5.0 years ago by daniel.silvestre70
5
votes
3
answers
8.7k
views
3
answers
Answer: A: How to properly sort GRanges?
... Firstly, verify that seqlevels are sorted: gr <- sortSeqlevels(gr) Then, just sort your GRanges object: gr <- sort(gr) Simple as that. You should take some time follow through the GenomicRanges vignettes. There are a lot of quite useful tricks inside ...
written 5.0 years ago by daniel.silvestre70
0
votes
1
answer
2.0k
views
1
answers
Comment: C: Quality filtering of exactSNP-generated VCF files
... For indels, I'm using the subjunc-generated indels file. The QUAL field there has other scale (I'm not sure exactly which scale, though). As we already had some independent clinical/laboratorial results, I've calibrated the parameters based on those previous findings. The expected indels were there. ...
written 5.0 years ago by daniel.silvestre70
0
votes
1
answer
2.0k
views
1
answers
Comment: C: Quality filtering of exactSNP-generated VCF files
... My parameters were based on guidelines used by GATK pipelines. They suggest at least 2 supporting reads to call a SNPs as a good candidate. Your parameters work fine. But, as we are using these results for clinical investigation, a more stringent criteria seems appropriate. About indels, I'm treatin ...
written 5.0 years ago by daniel.silvestre70
3
votes
1
answer
2.0k
views
1
answer
Quality filtering of exactSNP-generated VCF files
... I'm dealing with the results of some VCF files generated with exactSNP over BAM files made with subjunc aligner (all installed from Rsubread package) from a RNA-Seq project (made with HiSeq/TruSeq/mRNA only). Phred scores are the default (phred+33). The score scale of the FASTQ was detected as Sange ...
variantannotation exactsnp qc written 5.0 years ago by daniel.silvestre70 • updated 5.0 years ago by Wei Shi3.2k
2
votes
1
answer
615
views
1
answer
Failed assertion in subjunc aligner for large indels
... I'm currently using Rsubread (and the standalone programs) to process some RNA-Seq data. Everything seems OK, but some doubts emerged. After running the  subjunc aligner with this command: subjunc -i ../../genomes/UCSC/hg19/Rsubread/hg19.Rsubread.idx -r Thiago_ACTTGA_L008.fastq.gz --gzFASTQinput ...
rnaseq subjunc indel written 5.0 years ago by daniel.silvestre70 • updated 5.0 years ago by Wei Shi3.2k
1
vote
1
answer
3.3k
views
1
answers
Comment: C: Using DESeq2 with few biological replicates
... I´m aware of such design issues. As usual, I came into the project way after experimental runs. So, I'm trying to do my best and asking for some expert advice. I hope to convince PIs to (re)design things before next round of runs.  ...
written 5.1 years ago by daniel.silvestre70
0
votes
1
answer
3.3k
views
1
answers
Comment: C: Using DESeq2 with few biological replicates
... What's the size of a decently-sized control group? I don't expect very drastic expression changes as the focal gene don't regulate anything, AFAIK. But, case subjects have a quite altered chromosomal architecture.  ...
written 5.1 years ago by daniel.silvestre70
0
votes
1
answer
3.3k
views
1
answers
Comment: C: Using DESeq2 with few biological replicates
... For now, as a pilot, we have 3 healthy controls and 2 cases of Bloom's. The focal gene (BLM) is somewhat responsible for chromosomal integrity. Controls and one case were run on the same lane. The other case on other lane/cell. ...
written 5.1 years ago by daniel.silvestre70
4
votes
1
answer
3.3k
views
1
answer
Using DESeq2 with few biological replicates
... I have a couple of TruSeq/HiScanSQ mRNA-seq from blood samples (no globin depletion) from subjects with different rare autosomal recessive disorders related to nucleotide-excision repair or junction resolution. Of course, we have few biological replicates of each condition (e. g. only two with Bloom ...
rnaseq deseq2 written 5.1 years ago by daniel.silvestre70 • updated 5.1 years ago by Simon Anders3.6k

Latest awards to daniel.silvestre

Appreciated 4.3 years ago, created a post with more than 5 votes. For A: How to properly sort GRanges?
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Quality filtering of exactSNP-generated VCF files
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Using DESeq2 with few biological replicates
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: How to properly sort GRanges?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 392 users visited in the last hour