User: bhagyathimmappa

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Posts by bhagyathimmappa

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Gene predection or gene information extension from available gtf file.
... Thank you, I will try and let you know. ...
written 12 days ago by bhagyathimmappa0
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Comment: C: Scafolding and gap filling
... Thank you. I do not have any additional reads to use for scaffolding, all I have is illumina Mi-seq paired end data. I still just tried to use SSPACE with denovo assembled genome file and paired end data(same ones, used for denovo assembly). It resulted in exact same number of contigs observed in t ...
written 13 days ago by bhagyathimmappa0
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Answer: A: Scafolding and gap filling
... I have paired end reads from Mi-seq only, I do not have any other reads. To do scaffolding or gap filling I should have extra reads right? Whatever the reads I got from Mi-seq paired end sequencing I used for velvet denovo assembly. ...
written 14 days ago by bhagyathimmappa0
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Scafolding and gap filling
... Hello all, for one of the novel fungi, we did illumina mi-seq paired end sequencing and used velvet to assemble, I have 15500 contigs. some information about reads (after removing adapters and poor quality bases): Encoding : Sanger / Illumina 1.9 Total Sequences : 1747634 Sequence length : ...
assembly scafolding gap filling illumina written 14 days ago by bhagyathimmappa0 • updated 13 days ago by Sej Modha2.0k
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Answer: A: Gene predection or gene information extension from available gtf file.
... I have .fasta file which is my denovo assembly file. ...
written 17 days ago by bhagyathimmappa0
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Gene predection or gene information extension from available gtf file.
... #May be dumb question Hello all, for a given fungi there is assembly with 99contig and gtf file available, we have sequenced sensitive strain and did denovo assembly. For further work I need to generate gtf file for denovo assembly (sensitive strain for which we need to map gene location). I am ...
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Answer: A: Improving existing assembly using PacBIo reads
... Dear colindaven, I have used canu and tried to assemble, here is the global stats. PARAMETERS: ---------- 40 (expected coverage) 0 (don't use overlaps shorter than this) 0.000 (don't use overlaps with erate less than this) 1.000 (don't use overlaps with erate more than this) OVERLA ...
written 29 days ago by bhagyathimmappa0
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Answer: A: Polish PacBio assembly with latest PacBio tools : an affordable solution for eve
... Hello, Thank you for the post. Do you have any idea about how to improve available assembly using PacBio reads? ...
written 29 days ago by bhagyathimmappa0
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Comment: C: Improving existing assembly using PacBIo reads
... Thank you Kevin. Nice one, but it explains only about polishing, I want to know how to improve the scafolding using PacBio long reads. ...
written 29 days ago by bhagyathimmappa0
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Improving existing assembly using PacBIo reads
... Hello all, I am new to Bioinformatics field, I have an assembly available for one of the fungi (14.5mb) but this one is not end to end assembly. we have got the PacBio sequencing done for the same strain of an organism. a. I wan to check the quality of these reads (something like fastqc). b. I wan ...
assembly alignment tool sequencing written 4 weeks ago by bhagyathimmappa0

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