User: bzg

gravatar for bzg
bzg40
Reputation:
40
Status:
New User
Location:
Brazil
Last seen:
6 months, 1 week ago
Joined:
4 years, 7 months ago
Email:
e***********@gmail.com

Posts by bzg

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Can't find position in GnomAD VCF
... thanks Pierre for taking your time to test it! The only difference I could conceive is the way I uncompressed the file. I used the nautilus utility. I realized that the size is much smaller (73Gb) while uncompressing with gunzip (100Gb). ...
written 7 months ago by bzg40
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Comment: C: Can't find position in GnomAD VCF
... You used the complete vcf. I used only the 18th chromosome. Maybe that is the reason. ...
written 7 months ago by bzg40
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Can't find position in GnomAD VCF
... I have a set of 700 mutations that I need to download from GnomAD. My first problem was: the mutation rs489693 can be found in the browser but it is not present in the VCF file (gnomad.genomes.r2.1.1.sites.18.vcf.bgz). I searched also by the position 57882787. Why this mutation is not present in t ...
vcf snv gnomad written 7 months ago by bzg40 • updated 7 months ago by zx87548.7k
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Comment: C: How to fix the BAM file (SAM validation error)
... Dear Pierre, thanks very much for your answer, but, as I said in the question, I aware of that I can set VALIDATION_STRINGENCY=LENIENTE, but I want to fix my BAM file because it is another program that is calling it (Astrolabe, which I don't have the source). ...
written 19 months ago by bzg40
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Comment: C: How to fix the BAM file (SAM validation error)
... Thanks for the link: I will try the solution: java -cp /path/to/picard/bin/htsjdk-1.133.jar htsjdk.samtools.FixBAMFile source.bam fixed.bam (EDIT: it worked. Thank you so much! You saved me a lot of time) ...
written 19 months ago by bzg40
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How to fix the BAM file (SAM validation error)
... I get the following error when I try to build the index of my BAM file: Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 3009, Read name M00918:82:000000000-BMF6N:1:1101:10112:22298, bin field of BAM record does not equal value computed based on ...
alignment written 19 months ago by bzg40 • updated 19 months ago by Pierre Lindenbaum124k
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PROKKA: File .err - why all my features have inconsistent gene
... I am using PROKKA with the following set of arguments: `$ prokka myorganism.fa --cdsrnaolap ON --rfam 1 --rawproduct` While my gbk and gff seems okay, I obtain an error file of 1.2Mb saying that all my features have inconsistent gene locations and "DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding reg ...
genome annotation prokka written 2.6 years ago by bzg40
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Comment: C: BLAST Database error in TAXAassign
... Thanks! That solved the problem. ...
written 2.6 years ago by bzg40
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BLAST Database error in TAXAassign
... Dear all, I am testing TAXAasign and getting the following error: [esther@localhost testes]$ ~/Softwares/TAXAassign-master/TAXAassign.sh -t 70 -m 60 -a "60,70,80,95,95,97" -f test.fasta [2017-05-02 17:10:09] TAXAassign v0.4. Copyright (c) 2013 Computational Microbial Genomics Group, Univ ...
ncbi blast taxaassign written 2.6 years ago by bzg40 • updated 2.6 years ago by genomax75k
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Comment: C: Trouble with installation Trinity on Linux 32 bit
... maybe this helps: http://stackoverflow.com/questions/12591629/gcc-cannot-find-bits-predefs-h-on-i686 ...
written 2.9 years ago by bzg40

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