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Search: Posts Made By: kwtennis311
Forum: Bioinformatics 08-12-2010, 07:01 AM
Replies: 1
Views: 1,087
Posted By kwtennis311
BLAST Reference

When using the BLAST online tool, is there any way to use hg18/ncbi 36 instead of hg19/ncbi37?

Thanks
Forum: Bioinformatics 07-20-2010, 09:31 AM
Replies: 2
Views: 67,803
Posted By kwtennis311
Question sam to bam

I was sure this had been asked earlier, but could not find. Does anyone have a script to convert files from sam to bam format?

Thanks
Forum: Bioinformatics 06-30-2010, 09:51 AM
Replies: 0
Views: 1,504
Posted By kwtennis311
Question ELAND output quality score

The *_sorted.txt (among other) files give a quality score for each read. How exactly is that quality score computed? I understand that it is comes as a String with ASCII character code = quality...
Forum: Bioinformatics 06-15-2010, 06:23 AM
Replies: 5
Views: 2,992
Posted By kwtennis311
Alignment Visualization

I am looking for a way to align contigs from a de novo assembly against a reference genome and visualize which parts of the genome are covered. Any recommendations?

Thanks
Forum: Bioinformatics 06-15-2010, 06:16 AM
Replies: 1
Views: 2,791
Posted By kwtennis311
Question Alignment with Genome Studio

I have contigs from a de novo assembly that I want to align against a reference genome to check the accuracy of my assembler. Can Genome Studio be used to do/visualize this?

Thanks
Forum: Bioinformatics 06-11-2010, 11:06 AM
Replies: 4
Views: 13,404
Posted By kwtennis311
Thumbs up thanks

thanks guys, Biopython did the trick
Forum: Bioinformatics 06-10-2010, 11:39 AM
Replies: 4
Views: 13,404
Posted By kwtennis311
Question fastq to fasta conversion

How can I convert my fastq files to two fasta files with one containing the reads and another containing the quality scores?

Thanks :confused:
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