bedtools Posts

A: What is a better strategy for finding novel transcripts? by Amitm • 1.7k
Hi, I assume this is an organism for whom reference genome/ annotation are available. I have expe...
C: Is It safe to convert .bam to .fastq and re-do the analysis? by genomax ♦ 76k
As long as your BAM file contained unaligned reads (and they were not hard-clipped) you should be...
C: Denovo sequencing of species in different locations by genomax ♦ 76k
Having overly high coverage of data can be detrimental to assemblies as well (what is the genome ...
C: What is a better strategy for finding novel transcripts? by genomax ♦ 76k
Do you have a reference genome available? If so, reads from novel transcripts should still be map...
A: How to properly measure the length of a reference genome by John Marshall ♦ 1.9k
Even better and easier to use a tool that understands what's in a FASTA file. For example, index ...
A: Software for Gene ontology enrichment graph by snijeshvp • 0
[Webgestalt][1] [ClueGO][2] [1]: http://www.webgestalt.org/ [2]: http://apps.cytoscape.org...
A: How to properly measure the length of a reference genome by elcortegano • 20
I have noted that answer above counts the end line delimiters as characters, thus inflating genom...
C: Denovo sequencing of species in different locations by WouterDeCoster ♦ 42k
Of course, you will need to have enough RAM for your assembly. I also don't know the genome size ...
C: Denovo sequencing of species in different locations by biocon • 10
Due to size I spitted the data. If I combine all the lanes, the read size will more than 100 GB o...
C: only unique mapped paired-end reads by gb • 1.3k
Think you need to add `-F 2` to `samtools view`. Here you can find which options you have https:/...
A: Denovo sequencing of species in different locations by WouterDeCoster ♦ 42k
It would probably be better to have all reads available for your assembler at the same time, so I...
C: Software for Gene ontology enrichment graph by lessismore • 730
http://bioinfo.cau.edu.cn/agriGO/analysis.php here you can choose a customized annotation + cus...

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