User: cristianrohr768

Reputation:
30
Status:
New User
Location:
Spain
Last seen:
2 months, 2 weeks ago
Joined:
7 years, 2 months ago
Email:
c**************@gmail.com

about me

Posts by cristianrohr768

<prev • 19 results • page 1 of 2 • next >
0
votes
0
answers
119
views
0
answers
Fix t_coffee alignment with small sequence
... Hello, i have one DNA MSA [![msa.png](https://i.postimg.cc/023LLttW/msa.png)](https://postimg.cc/KRPqT5hB) Everything is were i expect to be, except for the second sequence, it's forced to be aligned in the ends. I tried several things (gapopen and extent values, local alignment) but i cannot find ...
t_coffee alignment msa written 3 months ago by cristianrohr76830
2
votes
2
answers
3.2k
views
2
answers
Fisher Strand in GATK, a good measure to detect Strand Bias?
... Hello, I follow the GATK good practices to call variants on 11 samples from a custom truseq design. I do Joint genotyping and apply Hard Filters to my data http://gatkforums.broadinstitute.org/discussion/2806/howto-apply-hard-filters-to-a-call-set. In a second test, i skip the joint genotyping ste ...
gatk strand bias fisher strand written 4.6 years ago by cristianrohr76830 • updated 8 months ago by Pablo Marin-Garcia1.8k
0
votes
1
answer
3.5k
views
1
answers
Comment: C: Usage of GATK Joint genotyping and filtering, or filtering and then joint genoty
... Hello @nchuang, I'm following the GATK best practices. To be able to use the VQSR you need a lot of samples, more than 30 exomes. In my case I just have 11 samples, from targeted sequencing, so I must stick to the hard filters. ...
written 4.6 years ago by cristianrohr76830 • updated 6 months ago by RamRS27k
0
votes
1
answer
3.5k
views
1
answer
Usage of GATK Joint genotyping and filtering, or filtering and then joint genotyping?
... Hello, I have 11 samples from a custom Truseq design I used HaplotypeCaller for my 11 samplesjava -jar /home/horus/Instaladores/GenomeAnalysisTK-3.4-0/GenomeAnalysisTK.jar -T HaplotypeCaller -R /home/horus/Escritorio/GATK/GATK/2.8/b37/human_g1k_v37.fasta -ERC BP_RESOLUTION -I $file/alineamiento/re ...
gatk joint genotyping filtering variants written 4.6 years ago by cristianrohr76830 • updated 4.6 years ago by nchuang210
3
votes
1
answer
2.2k
views
1
answer
Per base sequence quality before and after truseq adapters removal
... Hello all, I have Illumina Truseq data from a custom design sequenced on a MiSeq. Before removal of adapters sequences, quality from position starting to 85bp (reads of 151 bp) drops dramatically. After removal of the adapters sequences, quality is really high, more than at the start of the reads, ...
adapters illumina removal truseq written 4.6 years ago by cristianrohr76830 • updated 4.6 years ago by harold.smith.tarheel4.5k
0
votes
1
answer
2.7k
views
1
answer
Blast raw score calculation
... Hello, I search for the past two days, trying to find out how the blast raw score is calculated, i read i lot, read the answers here, but i can't found the right answer to my problem I'm using a 240 aa query, blastp agains refseq, the first result is   Range 1: 140 to 379 Score Expe ...
calculation raw score blast written 4.8 years ago by cristianrohr76830 • updated 4.1 years ago by Biostar ♦♦ 20
0
votes
2
answers
1.2k
views
2
answers
Estimation sequencing sustitution error rate
... Hi, i have data from a mtDNA sequencing on a 316 Ion PGM Chip. Sequence reads where mapped to rCRS reference assembly. With mitoSeek i get a table that looks like this  Chr                                               Loc    Ref    A    T    C    G    a    t    c    g gi|251831106|ref|NC_012920.1 ...
rate error sequencing written 5.2 years ago by cristianrohr76830 • updated 5.2 years ago by Brian Bushnell17k
0
votes
0
answers
2.0k
views
0
answers
Comment: C: Strange variant call it show a indel but looks like a SNP
... I don't know this is not allowed, what i must do? i can't delete the post in seqanswers ...
written 5.6 years ago by cristianrohr76830
0
votes
0
answers
2.0k
views
0
answers
Comment: C: Strange variant call it show a indel but looks like a SNP
... Not yet, i have a typo in the post, now i fix it, you can see that IGV you 5 insertions, they are the blue mark present in five reads, the same that are reported in SAR=5 ...
written 5.6 years ago by cristianrohr76830
0
votes
0
answers
2.0k
views
0
answers
Comment: C: Strange variant call it show a indel but looks like a SNP
... This is data from a ION PGM ...
written 5.6 years ago by cristianrohr76830

Latest awards to cristianrohr768

Popular Question 3.9 years ago, created a question with more than 1,000 views. For Usage of GATK Joint genotyping and filtering, or filtering and then joint genotyping?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For [Request] Case/Control VCF dataset
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Strange variant call it show a indel but looks like a SNP
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Fisher Strand in GATK, a good measure to detect Strand Bias?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Estimation sequencing sustitution error rate
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Missing genotypes, in case control study using Plink
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Per base sequence quality before and after truseq adapters removal
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Missing genotypes, in case control study using Plink
Popular Question 5.3 years ago, created a question with more than 1,000 views. For Blast Multifasta Against Ncbi Nr Database, And Download All The Results

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 894 users visited in the last hour