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Rahul Nayak commented on the blog Installing Salmon for Trinity !- Jit posted a new ad in the Opportunity Postdoctoral Research Assistant at RVC
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- Neel 1588 days ago
Using KAT again (You will need the modules:
KAT/2.1.1andgnuplot/4.6.5) – we can plot the kmer content of the assembly compared to the kmer content of the read set. The first thing we need to do is to combine the reads into a single file, for gzipped files, this can be done withzcat, or for unzipped filescat.Ex.
$ cat reads_R1.fastq >> combined.fastq $ zcat reads_R2.fastq.gz >> combined.fastqWe will now use
kat compto create a kmer content comparison. Usekat comp --helpto get help for the program, then create a comparison between the combined reads and the assembly. Make sure that you use the flags for canonical hashes for both sequence 1 and 2, as well as 8 threads. Finally, clean up you working directory by removing the combined fasta file, and re-zipping any unzipped files. Then download the output files to you computer usingscpand look at the png file that was produced.- Does the kmer content look good to you?
- How much of the kmer “noise” is part of the final assembly?
- What do you think contamination would look like in the kmer plot?
- What can the kmer graph tell you about the ploidy of the organism?
- Rahul Nayak published a blog post Installing Salmon for Trinity !Comments
- Rahul Nayak 2378 days ago
Sometime, you need to provide the path
➜ Tools git:(master) ✗ PATH=$PATH:/home/tools/anaconda3/bin
➜ Tools git:(master) ✗ export $PATH
- Jit bookmarked RNA-seq Analysis Workshop Course Materials
- Rahul Nayak posted to the wire
- Rahul Nayak created a new bio-script Perl subroutine to read genome/reads fasta file !
- Rahul Nayak published a blog post Installing Trinity !
- Sanjay is now a friend with Aaryan Lokwani
- Aaryan Lokwani is now a friend with Sanjay
