-
How could you use alignment data (and `samtools`) as well as `bedtools` in your own project?
Provide a least two examples of what said code might look like.
sr320 updated
7 years ago
-
Python exists with `Killed: 9` when attempting to load the E. coli GenBank record on local computer.
By rough calculation (thanks @RNAer ), there are ~260000 features in the record, and each feature i…
-
I am running into errors when using the test_ima.sh script to test my installation of iMetAMOS. The errors read:
Error, provided contig file does not exist: ftp://ftp.ncbi.nih.gov/genomes/Bacteria…
-
Hi,
There used to be a script named genome_setup.py that allowed you to use custom genomes with the bcbio-nextgen pipeline. I cannot find this script now, is it possible still somehow to do this? We'…
-
Hi,
I've installed Interpro on my Mac OS X and have attempted to execute a test run from my terminal as follows:
$ ./interproscan.sh -f TSV -i ~/Documents/interproscan-5.18-57.0/test_proteins_new.fa…
-
In talking with Zech and Jamie during a code review yesterday about the positional metadata problem (#1159), one thing that came up was incorporating support for graph-based representation of sequence…
-
I successfully downloaded and installed the latest get_homologues release:
```
$ perl install.pl
### 1) checking required parts:
## checking mcl-14-137 (lib/phyTools: $ENV{'EXE_MCL'})
>> OK
## c…
-
Coordinate with @tracykteal and @biobenkj.
-
- biological uses outside of the group: http://www.ncbi.nlm.nih.gov/sites/myncbi/1ruvipqAmaMkN/collections/48107393/public/
- tools building on khmer concepts: http://www.ncbi.nlm.nih.gov/sites/myncbi…
-
I'm aligning (in batches) around 20TB of read data against several thousand microbial genomes. Some of these batches fail with core dumps after a very long runtime (around 10x as long as those that a…