User: Hernán

gravatar for Hernán
Hernán110
Reputation:
110
Status:
Trusted
Location:
Argentina
Last seen:
2 months ago
Joined:
5 years, 5 months ago
Email:
h*************@gmail.com

I am a Bioinformatics Programmer in the Institute of Veterinary Genetics (IGEVET) of La Plata, Argentina. I work on a variety of projects in collaboration with people at the Institute, including analyzing phylogenetics data and occasional microarray data. I use Smalltalk, Shell Scripting, NoSQL and sometimes R, Perl and Python to analyze data from sequencing experiments.

Posts by Hernán

<prev • 24 results • page 1 of 3 • next >
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Bos taurus gc5 annotation for PennCNV not available or corrupted?
... My goal is to generate the .gcmodel file for a PennCNV script called **cal_gc_snp.pl** For this task one necessary input file is a "gc5" annotation file which can be downloaded from genome.ucsc.edu I tried to download the gc file from the [Table Browser][1], but every download has the limitation of ...
genome assembly gc cow cnv written 9 weeks ago by Hernán110
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Answer: A: Where to get >200Gb to build Bovine genome index in HISAT2?
... I've managed to build an index, this is the output of hisat2-inspect -s: Index version 2.1.0 Flags 1 2.0-compatible 0 SA-Sample 1 in 16 FTab-Chars 10 Sequence-1 AC_000158.1 158337067 Sequence-2 AC_000159.1 137060424 Sequence-3 A ...
written 3 months ago by Hernán110
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Comment: C: Where to get >200Gb to build Bovine genome index in HISAT2?
... Yes, I've tried to build the index locallly but failed with a lack of memory message. ...
written 3 months ago by Hernán110
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Comment: C: Where to get >200Gb to build Bovine genome index in HISAT2?
... No, that should be the begin of the output when the build is successful. ...
written 3 months ago by Hernán110
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Comment: C: Where to get >200Gb to build Bovine genome index in HISAT2?
... Yes please, I started a run in a server to see the initial output: > Settings: Output files: "UMD3.1.1.AC.idx.*.ht2" Line rate: 7 (line > is 128 bytes) Lines per side: 1 (side is 128 bytes) Offset rate: 4 > (one in 16) FTable chars: 10 Strings: unpacked Local offset > rate ...
written 3 months ago by Hernán110
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Comment: C: Where to get >200Gb to build Bovine genome index in HISAT2?
... Hi Wouter, Apparently HISAT2 cannot parse spaces after commas in the input chromosomes list? I removed spaces and re-uploaded the GCF_AC.txt and GCF_ACNW.txt. The output should be eight files named like these: UMD3.1.1.AC.idx.1.ht2, UMD3.1.1.AC.idx.2.ht2, UMD3.1.1.AC.idx.3.ht2, etc (Hopefully ...
written 3 months ago by Hernán110
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Comment: C: Where to get >200Gb to build Bovine genome index in HISAT2?
... You are right, the output is wrong because I've provided the input chr list not in the comma delimited format required by HISAT2. I've did this before but somehow uploaded old files to GitHub. Now I've re-uploaded the files in (hopefully) the correct format, however I don't want to abuse your kindn ...
written 3 months ago by Hernán110
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Comment: C: Where to get >200Gb to build Bovine genome index in HISAT2?
... I would be very grateful if you could get a slot in your facility. Please let me know if you ran into any issues. ...
written 3 months ago by Hernán110
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Comment: C: Where to get >200Gb to build Bovine genome index in HISAT2?
... I wrote a mail to hisat2.genomics@gmail.com some days ago but unfortunately still not received an answer. Maybe writing to him directly would help? ...
written 3 months ago by Hernán110
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Where to get >200Gb to build Bovine genome index in HISAT2?
... We are trying to index the UMD 3.1.1 Bovine genome using the [HISAT2][1] software. The problem is that we need more than 200 Gbytes of memory for the hisat2-build script, and we were unable to get enough hardware resources in the Argentine scientific computing network. We assume more than 200Gb bec ...
genome indexing next-gen rna-seq hisat2 written 3 months ago by Hernán110

Latest awards to Hernán

Popular Question 4.9 years ago, created a question with more than 1,000 views. For Checking Validity Of Dna Sequence In Bio* Toolkits?
Commentator 4.9 years ago, created a comment with at least 3 up-votes. For C: Checking Validity Of Dna Sequence In Bio* Toolkits?
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: How To Get Genbank File Using Bioperl
Autobiographer 4.9 years ago, has more than 80 characters in the information field of the user's profile.

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