User: Marvin

gravatar for Marvin
Marvin120
Reputation:
120
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Trusted
Location:
Australia
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1 month, 3 weeks ago
Joined:
3 years, 4 months ago
Email:
d****@gmx.de

Posts by Marvin

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Comment: C: snpEff: wrong HGVS output?
... yes, everything as expected here, c.-1032 is the correct HGVS notation (see the comments below Kevins answer) ...
written 7 weeks ago by Marvin120
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Comment: C: GRCh37.p13 download at NCBI FTP?
... I know how to get it from ensembl, I was curious where NCBI hides the equivalent :-) ...
written 7 weeks ago by Marvin120
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GRCh37.p13 download at NCBI FTP?
... I'm lost at the NCBI FTP server. Which file contains all chromosomes of GRCh37.p13 in one fasta? The program that I want to use takes one fasta file as the reference sequence. At ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens/ARCHIVE/ I don't see GRCh37.p13 and I don't see a README file .. I'm a little ...
ncbi grch37 reference written 7 weeks ago by Marvin120 • updated 7 weeks ago by Kevin Blighe31k
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Comment: C: snpEff: wrong HGVS output?
... I think this is a case of "either A or B". I was hoping for a confirmation but it's okay since I'm fairly confident that the NCBI made a mistake. Which is possible since their employees are humans, too :-) Thanks for your help! ...
written 8 weeks ago by Marvin120
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Comment: C: snpEff: wrong HGVS output?
... You correctly state that the 5' UTR is 1032 bases in length. This means that the coding sequence MUST start at 1033, right? But according to NCBI (https://www.ncbi.nlm.nih.gov/nuccore/NM_000314) the coding sequence ("Feature" -> "CDS") starts at position 1032. This doesn't match your observation. ...
written 8 weeks ago by Marvin120
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Comment: C: snpEff: wrong HGVS output?
... I think I've found the solution: the annotation on the NCBI page of NM_000314 is just wrong! They say that the CDS Feature starts at position 1032 of the transcript. However, in the UCSC / ensembl / NCBI genome browser, the 5' UTR starts at position 89,623,195 and the coding sequence starts at Posit ...
written 8 weeks ago by Marvin120
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Comment: C: snpEff: wrong HGVS output?
... Hi Kevin, how do you retrieve the information that the 5' UTR is 1032 bases in length? If you navigate to the NM_000314 page at NCBI you will find that the coding sequence starts at Position 1032 (look for "CDS" Feature). Thus the 5' UTR is 1031 bases in length, not 1032. ...
written 8 weeks ago by Marvin120
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snpEff: wrong HGVS output?
... When I go to UCSC table browser and get the BED file for NM_000314.6 (gene = "PTEN"), I find out that the first exon starts at position 89623194 in GRCh37/hg19 (!). Thus the exon starts at 89623194+1 = 89623195 in a 1-based coordinate system. Now I've created an artificial VCF file: ##fileform ...
hgvs snpeff written 8 weeks ago by Marvin120 • updated 7 weeks ago by WouterDeCoster33k
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Illumina: Why does a flow cell have lanes?
... I've just wondered: why not just all adapters on one big plate? I'm a bioinformatician, so I apologize in advance if the answer is obvious to wet lab scientists. ...
sequencing written 9 weeks ago by Marvin120 • updated 9 weeks ago by genomax58k
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Comment: C: why do bed files not contain information about the reference?
... thanks everyone for bringing all the details together :) ...
written 3 months ago by Marvin120

Latest awards to Marvin

Popular Question 7 weeks ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: NGS mapper that supports IUPAC reference
Popular Question 16 months ago, created a question with more than 1,000 views. For I don't understand bcftools call behaviour
Popular Question 16 months ago, created a question with more than 1,000 views. For Samtools mpileup: read base column symbols
Popular Question 16 months ago, created a question with more than 1,000 views. For IGV genome browser problems
Popular Question 16 months ago, created a question with more than 1,000 views. For NGS mapper that supports IUPAC reference
Popular Question 16 months ago, created a question with more than 1,000 views. For Split BAM into 1 BAM per contig
Popular Question 3.0 years ago, created a question with more than 1,000 views. For FASTA of an arbitrary genome: Is the first base the 5' end?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For IGV genome browser problems
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Get the consensus sequence ... (I know, should be easy)
Student 3.0 years ago, asked a question with at least 3 up-votes. For NGS mapper that supports IUPAC reference

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