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The choice of the cell viability assay using crystal violet staining was based on a previous work [ 32] with modification of reading A595 nm.
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No evidences of multiple copies (size variation, modifications of reading frame) were found for any fragment.
Known heterozygous sites, at which two or more histone modifications displayed significantly different proportions of reads carrying each allele, were identified.
The output of the digital normalization script is a downsampled set of reads, with no modifications to the individual reads.
The editing frequency was calculated as the number of reads containing the A-G modification divided by the total number of reads corresponding to the same miRNA.
The number of reads, the respective percentages, and the type of modification is listed for each event.
Once read classes are constructed, we only need a small modification of the E-step of IsoEM to use read classes instead of reads.
Indeed, these modifications reduced the occurrence of "mixed fragments" to negligible levels (less than 0.00025% of reads) in the CRoPS run reported here.
(B ) The number of reads with 3, 4, and 5 consecutive identical mismatches for each possible modification type.
The number of reads per kilobase per million reads (RPKM) method was used to calculate the modification levels of unique genes (BGI, Shenzhen, China).
Multilocus sequence types (MLSTs) were identified by mapping the reads against all M. abscessus allele variants held in the Institut Pasteur MLST database (http://www.pasteur.fr/recherche/genopole/PF8/mlst/) using a modification of the short-read sequence typing [ 26].
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