User: dp

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dp10
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Posts by dp

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goatools: how to write out (or draw) the entire GO hierarchy for all genes from one species (human)?
... I am trying to write out the entire GO hierarchy for humans using goatools. I don't have much experience with the package. I know that `read_ncbi_gene2go("assoc", taxids=[9606])` outputs a dictionary of human genes: GO id sets association with those genes but can't figure out how to organize and ou ...
goatools go written 4 months ago by dp10 • updated 3 months ago by dvklopfenstein0
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comparing sets of contigs
... Hi all I want to compare contigs assembled from two metagenomic samples that I expect to be similar. For each contig in one of the assemblies I would like to find any contig(s) in the other that it matches and vice versa. I tried building a BLAST db of one and then using blastn to query for the con ...
metagenomics sequence comparison blast written 6 months ago by dp10
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Comment: C: Reverse complements in BWA
... Thanks. Ineresting that even the small number of differences makes a difference when looking for paths in the graph formed by contigs and the paired-end reads connecting them. I guess the 1300 or so differences in the paired reads makes the difference. Wish I knew why there's a difference depending ...
written 9 months ago by dp10
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Comment: C: Reverse complements in BWA
... I don't know how to find the differences - that is what I asked. Using flagstat as you suggested I get: 3214312 + 0 in total (QC-passed reads + QC-failed reads) \\ 3214312 + 0 in total (QC-passed reads + QC-failed reads) 3183485 + 0 mapped (99.04%:-nan%) \\ 3183473 + 0 mapped (99.04%:- ...
written 9 months ago by dp10 • updated 9 months ago by Devon Ryan86k
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Comment: C: Reverse complements in BWA
... @istvan - I did this with no change, as expected. There aren't two datasets, there is one dataset which is in a fastg file so it contains the forward and reverse complement sequence of every node. I create a fasta file by dumping half of these. In one case I keep only the forward sense nodes, in t ...
written 9 months ago by dp10
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Comment: C: Reverse complements in BWA
... @Istvan - no, the other parts of the pipeline are deterministic: First I assemble the reads, then, because the fastg format for assembly graphs contains both the forward and reverse complement sequences for each edge, I remove one, then I align the reads to the contigs to create a graph of paired e ...
written 9 months ago by dp10
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Comment: C: Reverse complements in BWA
... Yes, downstream I am using the alignments of the reads to bridge between contigs in the assembly graph and have different results. I was surprised to see that these results are different depending on whether I use the sense or anti-sense sequence but so far the only difference I've been able to trac ...
written 9 months ago by dp10
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Comment: C: Reverse complements in BWA
... Thanks @Devon. Why would that be the case, doesn't the aligner align both the read and it's reverse complement to the contig? If the forward sense read maps in multiple places wouldn't the reverse complement map to the same places? Also - what is the best way to check this, I've been dumping the al ...
written 9 months ago by dp10
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Reverse complements in BWA
... I am aligning paired end reads to contigs from an assembly using BWA and it looks like I get different results if I use the contigs or their reverse complements. Does this make sense? Which result should I use since they are different? ...
reads alignment sequence written 9 months ago by dp10

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