Activity for Ben Langmead
-
Ben Langmead modified ticket #335
Invalid SAMFLAG for paired alignment
-
I know this is a long time coming, but we finally looked into this and we think the...
-
Bowtie2 segfault
-
That error is often because memory is exhausted. Can you tell us more about how big...
-
This is because the pseudo-random number generator is initialized fresh for each...
-
Results on reverse complement reads
-
Hi Francesca, Bowtie 2 is not guaranteed to find all valid alignments. It uses heuristics...
-
Thanks for these helpful reports! Val and I just fixed this in the bugs/313 branch,...
-
Hi Marc, When you are calculating the ending referencing coordinate of an alignment,...
-
Hi Felix, A couple questions. Are the Ns distributed fairly evenly across the genome?...
-
Our fault -- we included the ChrY-contigs and contigs.SHOTGUN_ONLY FASTA files, both...
-
Hi Devon, We see the cause of the problem. Basically, Bowtie 2 always searches for...
-
Zebrafish pre-built assembly
-
Such an index is available through iGenomes: http://support.illumina.com/sequencing/sequencing_software/igenome.ilmn....
-
prebuilt index for Dog
-
Now available on Bowtie site and on iGenomes: http://bowtie-bio.sourceforge.net/index.shtml....
-
sanger-fastq
-
I don't see "-" in modern FASTQ files, so I will close this. Ben
-
Nucleotide-to-protein alignment
-
PADUA has this functionality now. No plans to implement it within Bowtie, since good...
-
Colorspace mapping
-
More info for building from source section in the manual
-
Valentin Antonescu added some of the relevant documentation and we now provide 64-bit...
-
64-bit windows version
-
This is now available in the latest versions of Bowtie and Bowtie 2. Best, Ben
1