User: cschu181
cschu181 • 990
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Posts by cschu181
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... Why do you use the * at the end of your index? ...
written 5 hours ago by
cschu181 • 990
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... Edit: Yeah, never mind. ...
written 3 days ago by
cschu181 • 990
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... Maybe align them with some short/long read aligner (bwa mem, minimap, bbmap, ...) and visualise the results in a genome browser (IGV). Concerning your exon sequences, if they align to the same position then they must be similar if not partially identical. According to OMIM, ESR contains only 8 exons ...
written 4 days ago by
cschu181 • 990
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... If you want to produce a multiple alignment, just add all your sequences into the original fasta file from the beginning. Then again, this does not sound like a typical multiple alignment task. You could just do pairwise alignment of each exon sequence against the gene with e.g. emboss water. How ma ...
written 4 days ago by
cschu181 • 990
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... That's what I wrote in my first comment. I don't know about ONT, but of course Pacbio will introduce erroneous kmers due to their indel error model. ...
written 5 days ago by
cschu181 • 990
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... I don't think long reads would be an issue, it would just treat it as single-end fastq. When I look at Table2 in the centrifuge paper, kraken is about twice as fast as centrifuge, albeit with a much worse memory requirement (and of course the database creation takes ages). ...
written 5 days ago by
cschu181 • 990
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... kraken? Although, with PacBio you might have a problem with erroneous k-mers. ...
written 5 days ago by
cschu181 • 990
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... Make a multiple alignment (ClustalO, MAFFT, MUSCLE, ...), visualize and curate the alignment (remove gap columns, outlier sequences; JalView), use the alignment to calculate a tree (RaxML, PHYLIP), visualise the tree (iTOL). ...
written 11 days ago by
cschu181 • 990
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... What are the sequencing platforms in question? Some assemblers (e.g. unicycler for bacterial/microbial data) can take reads from different sources as input, e.g. for scaffolding. ...
written 14 days ago by
cschu181 • 990
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Comment:
C: PacBio Genome assembly
... You know, H. sapiens is not really the big dude when it comes to genome size :P ...
written 18 days ago by
cschu181 • 990
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