User: marongiu.luigi
marongiu.luigi • 450
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Posts by marongiu.luigi
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C: Blast: do separators matter?
... Ok, it makes sense. And for running a concatenated sequence versus the individual sequences, would the former provide any kind of computational improvement? Thank you ...
written 5 weeks ago by
marongiu.luigi • 450
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C: Blast: do separators matter?
... No, I would like to know whether this approach is viable or biased. The idea to concatenate was to have more specific results (a slightly better e-value) but also to ease the computation: instead of running blast (which takes a lot of time to run) n times for n sequences, launching it just once with ...
written 5 weeks ago by
marongiu.luigi • 450
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Comment:
C: Blast: do separators matter?
... Thank you, so I gather I should use '-' and not 'N' ...
written 5 weeks ago by
marongiu.luigi • 450
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... Hello,
If I have two sequences like this:
> seq 1
CCGCAGTAACGATATCCTTCGCCAGGCTTCCGCTTATTTTGCGAAGGCGGAGTTCGACCG
> seq 2
TCAGCAACAGCGACATCATCCGGATAAACGCAGTGCCCGTGCGCAGCGCGATGACTGGCTGAAGAAAGAGATACAGCGCGTATACGATGAAAATCACAAGG
that should map on the same organism, and I would like ...
written 5 weeks ago by
marongiu.luigi • 450
• updated
5 weeks ago by
Mensur Dlakic • 3.0k
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... The rationale of generating a consensus was exactly that of overcoming possible divergences against the reference sequence, given the high variability of viruses. Using hard clipped reads to make the consensus would be better? And are the 'N' introducing an error in the blast search? Thank you ...
written 6 weeks ago by
marongiu.luigi • 450
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... Because, in mapping viral sequences, there is the risk of calling viral what is either human or bacterial, thus one needs to run multiple rounds of blast on top of BWA MEM to remove false positives. I have tried to replicate the pipeline that is reported for instance in [Norman et al. Cell 2015][1]: ...
written 6 weeks ago by
marongiu.luigi • 450
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... No, the contigs or clusters I generated. ...
written 6 weeks ago by
marongiu.luigi • 450
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... In the graph, as in reality, I used reads 1,2,3 to make the consensus (contig) 1, then read 4 for contig 2 and reads 5,6 for contig 3, then simply concatenated everything with the spacer 10xN into cluster 1. Shal I re-run making a further consensus with the reference sequence and the three contigs? ...
written 6 weeks ago by
marongiu.luigi • 450
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... the aim is to confirm the mapping of the reads. Apologies for the term `clustal` I always get confused. I only used `clustal omega` to generate the consensuses. All the rest is about `BLAST`. ...
written 6 weeks ago by
marongiu.luigi • 450
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... but then I have to go into thousands of reads to check that. What I have done was to sort the reads by starting point and to call the reads into separate contigs if the starting point of the read n+1 was greater than the end point of the read n. I then used 10 Ns to separate the contigs ...
written 6 weeks ago by
marongiu.luigi • 450
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