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Search: Posts Made By: yekwah
Forum: Bioinformatics 11-11-2013, 01:56 PM
Replies: 5
Views: 2,135
Posted By yekwah
Thank you so much for this! The second...

Thank you so much for this!

The second option seems to be the best, though I would like to be as memory efficient as possible. I'm not entirely sure what a generator function is, so that might be...
Forum: Bioinformatics 11-11-2013, 12:40 PM
Replies: 5
Views: 2,135
Posted By yekwah
Thanks. I've fixed the indentation for the code...

Thanks. I've fixed the indentation for the code now, so hopefully that will help.

I'm pretty certain that if I keep calling SeqIO.write that I overwrite whatever I had already. It seems like when...
Forum: Bioinformatics 11-10-2013, 07:29 PM
Replies: 5
Views: 2,135
Posted By yekwah
Adding features to a multi entry genbank

I'm attempting to add features using BioPython to a multi-entry Genbank. Each entry in the genbank is a contig, and I'd like to annotate some BLAST hits.

I've performed a BLAST of my query against...
Forum: Bioinformatics 10-17-2013, 04:03 PM
Replies: 3
Views: 2,108
Posted By yekwah
The bowtie2 commands I specified were these: ...

The bowtie2 commands I specified were these:

bowtie2-build ref base_name
bowtie2 --sensitive-local -x base_name -1 fq1 -2 fq2 -S sam

I'm aware that Nterm and Cterm have particular meanings,...
Forum: Bioinformatics 10-16-2013, 05:27 PM
Replies: 3
Views: 2,108
Posted By yekwah
Unable to find flag in SAM with bowtie2 - but can with BWA

I'm currently using Bowtie2 to map my reads to a small region of a genome to find what region it's in by collecting the unmapped pairs of the reads which have mapped.

I'm currently using samtools...
Forum: De novo discovery 07-14-2013, 05:23 PM
Replies: 1
Views: 2,685
Posted By yekwah
Combining two different assemblies

Just wondering if anyone knows of any programs which can combine two different assemblies?

I've got paired end Illuminia data that I've assembled using Velvet and SPAdes. Once I fiddled with some...
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