User: bsp017

gravatar for bsp017
bsp01720
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New User
Location:
Wales, Bangor, Bangor Uni
Last seen:
4 days, 4 hours ago
Joined:
2 years, 2 months ago
Email:
b*****@bangor.ac.uk

Posts by bsp017

<prev • 4 results • page 1 of 1 • next >
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how to calculate genome coding density
... Hi all, I have just calculated gene coding desnsity across some bacterial genomes. It is coming out quite high at ~87%, I think it is usually around 80%. I simply counted the ATGC's in my .ffn file and subtracted that from the total nucleotide count. When calculating coding density should I includ ...
genome assembly rrna written 6 weeks ago by bsp01720
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length of combined transcripts
... Hi all, Is there a tool to calculate the combined length of transcripts which map to a given interval. For example as a function of bedtools or htseq? I can calculate the number of reads mapping to a particular gene using these tools but not the length of the gene segment which has been covered. Wh ...
rna-seq written 22 months ago by bsp01720 • updated 22 months ago by Alex Reynolds20k
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Answer: A: metatranscriptomic read mapping
... In response to my question, I found this paper; http://t.co/snb0U82HVZ which maps metatranscriptome files against an antibiotic resistance gene database. If reads map more than 3 times to a gene and span > 200 bp of that gene then it's considered significant.   ...
written 2.1 years ago by bsp01720
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metatranscriptomic read mapping
... I mapped a depleted metatranscriptome bam file against a reference bacterial genome. Some genes have a 'substantial' number of reads mapping. I have previously isolated this bacteria from the sequencing site. Is there a method where I could say that x number of genes from this bacteria are expressed ...
alignment rna-seq written 2.2 years ago by bsp01720 • updated 2.1 years ago by Brian Bushnell14k

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Popular Question 27 days ago, created a question with more than 1,000 views. For metatranscriptomic read mapping

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