Overview of repeat/Rfam
To compare the read expression in different repeat/Rfam families, we count the number of abundant reads in each family and plot the relative proportion.
- Rfam
- We catalogue noncoding RNA genes in Rfam annotation into five big classes: tRNA, rRNA, snRNA, ACA_snoRNA, CD_snoRNA and others. Note that miRNA annotations are excluded in the Rfam noncoding RNA analyses, for the reason that we have already obtained the miRNA read mapping information in 5.5.3. All rfam annotation files are downloaded from Rfam database [5], please see section 6.1 for more details.
- Repeat
- ncPRO-seq uses repeat annotations from http://www.repeatmasker.org/ RepeatMasker [14] results, see section 6.2 for the preparation of the annotation file. We classify different repeats based on the name of repeat family.
Chongjian Chen
2012-01-26
