User: O. William McClung

Reputation:
0
Status:
New User
Last seen:
1 week, 1 day ago
Joined:
1 month, 3 weeks ago
Email:
o********@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by O. William McClung

<prev • 5 results • page 1 of 1 • next >
0
votes
1
answer
51
views
1
answer
Consensus sequence from BAM file
... I have a `.bam` file which aligns reads against a reference genome. The locations of the reads partition themselves into a small number of clusters. Can BioConductor be used, perhaps with other tools such as samtools, to compute a consensus sequence for each cluster? ...
bam consensus written 21 days ago by O. William McClung0 • updated 8 days ago by Hervé Pagès ♦♦ 14k
0
votes
2
answers
92
views
2
answers
Answer: A: Can GenomicRanges findOverlaps ignore seqnames?
... @ Hervé: Many thanks. This solution clearly works. @ Hervé and Michael: Thanks for pointing out this use case should never occur. I need to go back and rethink my pipeline. ...
written 6 weeks ago by O. William McClung0
2
votes
2
answers
92
views
2
answers
Can GenomicRanges findOverlaps ignore seqnames?
... `findOverlaps` in the `GenomicRanges` package has a flag, `ignore.strand=TRUE`, which allows the overlap computation to use only the duple `(seqnames,ranges)`, essentially ignoring the strand. Is there a way to use `findOverlaps` to ignore `seqnames` so that only the duple `(ranges,strand)` is used ...
genomicranges findoverlaps written 6 weeks ago by O. William McClung0
0
votes
2
answers
127
views
2
answers
Answer: A: TxDb error: external pointer is not valid
... Thanks go to Martin Morgan for providing the correct answer. This works: ``` human_txdb <- makeTxDbFromGFF(file = "human.gff",format="gff3") saveDb(human_txdb,file = "human_txdb.sqlite") # export human_txdb <- loadDb(file = "human_txdb.sqlite") # import ``` ...
written 7 weeks ago by O. William McClung0
3
votes
2
answers
127
views
2
answers
TxDb error: external pointer is not valid
... On my box within R I attempted to create a `TxDb` object from a `GFF` file with ``` human_txdb <- makeTxDbFromGFF(file="human.gff",format="gff3") ``` and this crashed the R process. (Presumably an out-of-memory error.) Here's my environment: ``` R version 3.6.1 (2019-07-05) Platform: x86_64-pc-li ...
genomicfeatures software error written 8 weeks ago by O. William McClung0

Latest awards to O. William McClung

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 400 users visited in the last hour