User: star715

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star71520
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Posts by star715

<prev • 11 results • page 1 of 2 • next >
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error loading gff3 file to chado database
... I used the following command to load annotations from a gff file to chado database: gmod_bulk_load_gff3.pl --organism --gfffile --remove_lock The file runs but creates the following error for every CDS feature it processes: ``` this shouldn't happen in modified_uniquename at /Library/Perl/ ...
gmod chado database gff3 written 1 day ago by star71520 • updated 1 day ago by h.mon30k
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Comment: C: How can I fix frameshift errors in assembled genome?
... It is pacbio RSII data and I have been using hgap3/hgap4 to assemble it. I tried with flye but it gave more frameshift errors. Can pilon/Racon work with only pacbio data and no short reads? ...
written 4 months ago by star71520
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How can I fix frameshift errors in assembled genome?
... I have a genome assembled from pacbio reads. However I have noticed many frameshift mutations in the genome due to which some genes are not annotated even if they are present in the genome. How would I be able to fix it? ...
assembly genome polishing pacbio written 4 months ago by star71520 • updated 4 months ago by predeus1.4k
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Comment: C: Polishing genome with pacbio reads
... Because the data is RSII and arrow does not seem to support it. Yes it is a bacterial genome ...
written 5 months ago by star71520
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Polishing genome with pacbio reads
... Hi, I am trying to assemble some genomes from pacbio reads using HGAP3 followed by quiver polishing. However, even after multiple rounds of quiver polishing, I cannot attain quality value 50 (QV50) for a genome. QV50 seems to be recommended and I am able to get upto QV30 only. I have done polishi ...
quiver pacbio assembly written 5 months ago by star71520
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Comment: C: bacterial genome circularization
... Yeah I could assemble into a single contig. And yes, it has a reference. ...
written 7 months ago by star71520
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bacterial genome circularization
... I want to circularize bacterial genomes assembled via HGAP (from long reads obtained from pacbio sequencing). Circlator however fails to circularize it. What could be other options given I have only long reads? Also, if there is some way to fix the performance by circlator (I am using default circl ...
genome circlator bacteria circularization written 7 months ago by star71520
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Assemble multiple contigs to single
... Hi, I assembled pacbio reads using SMRTlink and got 15 contigs. When I blast them with each other, it seems they share 30-50% of the regions among each other. Now I do not know how to assemble them together to make a long contig. How can I reduce the number of these contigs? ...
contigs microbial pacbio genome assembly written 9 months ago by star71520
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Genome assembly of pacbio reads with SMRT Link
... I have been trying to do a genome assembly of a microbial genome around 9Mbp. I am using **SMRT Link** for the purpose. Can anyone suggest me the best selection of parameters **(seed length cutoff, FALCON cfg overrides, seed coverage, minimum concordance)** for a good assembly of the genome of that ...
pacbio hgap tool smrtlink genome assembly written 9 months ago by star71520 • updated 7 months ago by Biostar ♦♦ 20
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blast makedb database creation error
... I wanted to create a blast database using the command: makeblastdb -in filename.fasta -input_type fasta -dbtype prot -parse_seqids -out filename.fasta -title xyz but I got an error saying > BLAST Database creation error: Near line 65951, the local id is too > long. Its length is 51 but ...
database blast written 15 months ago by star71520 • updated 14 months ago by Biostar ♦♦ 20

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Popular Question 4 months ago, created a question with more than 1,000 views. For blast makedb database creation error

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