User: kristina.mahan

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Posts by kristina.mahan

<prev • 62 results • page 1 of 7 • next >
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Comment: C: Blobtools output files
... entire assembly is ~2000 contigs. no-hits: 594 contigs Bacteria: 252 contigs Proteobacteria: 817 contigs Haptista: 6 contigs Chordata: 17 contigs Euglena: 1 contig Ascomycota: 3 contigs Streptophyta: 7 contigs Chlorobi: 1 contig Chlorophyta: 36 contigs Most all the Proteobacteria have the same GC ...
written 10 days ago by kristina.mahan100
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Comment: C: Distinguishing sequencing reads as prokaryotic or eukaryotic without a reference
... So then you just remove the contigs that are the bacteria from the assembly (green in blobplot)? ...
written 10 days ago by kristina.mahan100
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Comment: A: Blobtools output files
... and which contigs are contaminants and need to be removed? ...
written 10 days ago by kristina.mahan100
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Blobtools output files
... ![blobtools graph #1][1] ![blobtools graph #2][2] Can somebody interpret these blobtools graphs please. My genome is an algal species. ![https://ibb.co/ZmgD7K8][3] ![https://ibb.co/mNf8GBw][4] [1]: https://ibb.co/mNf8GBw [2]: https://ibb.co/ZmgD7K8 [3]: https://i.ibb.co/PQWH04h/Screen-S ...
blobtools genome assembly contamination written 10 days ago by kristina.mahan100
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How to use gff file of old annotation to annotate new assembly
... I have a .gff file someone gave me from an old chloroplast annotation. How can I use that annotation file to annotate my chloroplast genome assembly? ...
annotation chloroplast genome gff written 15 days ago by kristina.mahan100 • updated 14 days ago by shelkmike280
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Comment: A: Illumina reads mapped back onto contigs have gaps
... Would you expect that contaminant contigs that have not yet been removed- would have gaps in coverage or less coverage? ...
written 15 days ago by kristina.mahan100
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Comment: C: Illumina reads mapped back onto contigs have gaps
... The illumina sequencing is 2 x 150 bp. The assembly was with pure pac bio reads. I could polished the pac bio assembly using illumina reads with pilon and see if that helps. But I will also try to map illumina reads without trimming or with different trimming parameters. ...
written 24 days ago by kristina.mahan100
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Comment: C: Illumina reads mapped back onto contigs have gaps
... I trimmed the illumina reads for quality and to trim the adapters. I used Trimmomatic with these parameters: LEADING:10 TRAILING:10 SLIDINGWINDOW:5:30 MINLEN:150 The genome size is ~ 200 Mb These are the results from trimming of the illumina reads: Input Read Pairs: 128614698 Both Surviv ...
written 24 days ago by kristina.mahan100 • updated 15 days ago by lieven.sterck8.7k
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Illumina reads mapped back onto contigs have gaps
... I assembled a genome using pac bio reads with the Flye Assembler. I then mapped my cleaned up illumina reads using bwa-mem onto the longest contigs and there is gaps in the contigs. Why is this? ...
illumina mapping written 24 days ago by kristina.mahan100
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Comment: C: How to reduce Quast stats being based on "contigs of size > 100000 bp"
... yes definitely. It says you can specify contig length but default is 500. I am not specifying contig length and the report says that the stats are based on contigs >= 100,000. So I am not sure what is happening. ...
written 7 weeks ago by kristina.mahan100

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Popular Question 10 days ago, created a question with more than 1,000 views. For Issues with mapping reads onto Reference genome using bwa mem
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