User: freddiejung

gravatar for freddiejung
freddiejung30
Reputation:
30
Status:
New User
Location:
Japan
Last seen:
11 months, 3 weeks ago
Joined:
4 years, 4 months ago
Email:
f**********@gmail.com

Posts by freddiejung

<prev • 19 results • page 1 of 2 • next >
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augustus Bam2hints program creates an empty .gff file
... Dear all, I am now making gene model using augustus v3.3.1. I have multiple RNA-seq data, so I tried to make hints using those data. When I tried to make intron hints according to this page ([http://bioinf.uni-greifswald.de/bioinf/wiki/pmwiki.php?n=IncorporatingRNAseq.Tophat][1]), I found bam2hin ...
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How to fix .bam file that was diagnosed as "MISSING_READ_GROUP" by Picard ValidateSamFile
... Hi, I am using Pilon to polish and elongate my PacBio assembly. But I realized Pilon always generate error like shown in the bottom. I found that one of my .bam file have something wrong and I performed Picard ValidateSamFile. This program diagnosed this .bam is missing group(↓). ## HISTO ...
pilon picard validatesamfile bam written 19 months ago by freddiejung30 • updated 13 months ago by oriolebaltimore130
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Comment: C: Racon generated an error like "terminate called after throwing an instance of 's
... Dear jean.elbers, I contacted the developer followong your advice (https://github.com/isovic/racon/issues/65). It turned out to be a gcc bug and the developer showed a solution. Best regards, Jung ...
written 19 months ago by freddiejung30
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Racon generated an error like "terminate called after throwing an instance of 'std::system_error'"
... I am using RACON(https://github.com/isovic/racon) to call consensus sequence of a genome. I get the following error: terminate called after throwing an instance of 'std::system_error' what(): Enable multithreading to use std::thread: Operation not permitted zsh: abort racon reads ...
software error assembly long-read written 19 months ago by freddiejung30
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PacBio long read error correction tools
... Dear all, in my previous post (https://www.biostars.org/p/303214/#303734), some people suggested that it's better to correct errors in log reads from PacBio sequel using short reads from illumina ahead of the genome assembly. I happened to find that the assembly with only short reads contains lo ...
long-read pacbio error-correction short-read written 20 months ago by freddiejung30 • updated 20 months ago by lieven.sterck6.2k
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Comment: C: Pipeline for hybrid genome assembly of long and short reads AND how to deal with
... Dear Carambakaracho, Thank you for detailed information. Actually, I used HGAP4 using only PacBio long-reads. It gave me the assembly with N50 = 22Mb and I thought it was better than I expected. Now I'm very excited about how much the assemble will be improved by using PILON like polishing softw ...
written 20 months ago by freddiejung30
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Comment: C: Pipeline for hybrid genome assembly of long and short reads AND how to deal with
... Dear erwan.scaon, Thank you for information. Is that better to correct error in long-reads BEFORE assembly than AFTER assembly? ...
written 20 months ago by freddiejung30
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Comment: C: Pipeline for hybrid genome assembly of long and short reads AND how to deal with
... Dear jean.elbers, Sorry for late reply and thank you for useful information. miniasm-racon-pilon pipeline looks good. I will give it a try. ...
written 20 months ago by freddiejung30
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Pipeline for hybrid genome assembly of long and short reads AND how to deal with PacBio sequel data
... Dear all, I am involved in the genome project of a insect species. The genome size of our species is estimated to be 500Mb and I have 100x illumina short read data and 50x Pacbio Sequel long read data. I have two questions: 1. I’m going to take hybrid assembly strategy. I thought ALPACA pipeline ...
genome illumina hybrid assembly pacbio assembly written 20 months ago by freddiejung30 • updated 20 months ago by Carambakaracho1.9k
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RepeatMasker:understanding buildSummary.pl output
... Dear all, I have a question about buildSummary.pl output file. I masked the repetitive sequences of my species with RepeatMasker and then, to summarize the ".out" file, run the buildSummary.pl. The output was like this:   Class Count bpMasked %masked ===== ...
genome repeatmasker written 3.9 years ago by freddiejung30

Latest awards to freddiejung

Popular Question 12 months ago, created a question with more than 1,000 views. For getting "std::bad_alloc" message when using filterBam (augustus3.1)
Popular Question 13 months ago, created a question with more than 1,000 views. For getting "std::bad_alloc" message when using filterBam (augustus3.1)
Popular Question 16 months ago, created a question with more than 1,000 views. For getting "std::bad_alloc" message when using filterBam (augustus3.1)
Popular Question 2.5 years ago, created a question with more than 1,000 views. For getting "std::bad_alloc" message when using filterBam (augustus3.1)

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