However, when the two SNVs occur close enough that the distance is less than the library insert size, haplotypes can be inferred by using the reads or read pairs spanning multiple SNVs (Fig. 1, A1 and B1).
To identify genes showing significant changes in expression between the two libraries, the expression level of each unigene was determined by using the reads per kb per million reads (RPKM) method [ 36].
Together, these data show that anti-CCP/MCV-negative multiplex-positive RA patients cannot be distinguished from anti-CCP/MCV-negative multiplex-negative RA patients by using the read-outs described.
Expression of each individual gene was quantified by using the Reads Per Kilobase per Million mapped reads (RPKM) method.
After de-multiplexing the bulk of the NGS read data into 96 pools by using the indexes, read mapping on the reference gene sequences was conducted separately pool-by-pool.
By using the long reads only for the validation of the TR patterns, MixTaR is robust with respect to the error rate of long reads.
For example, we may estimate α by using the all the read sequences or by using information from other dedicated studies about sequencing and mapping errors.
The contigs having homology to the reference were extended by using the original reads with Velvet.
For all mapped genes with unique matched reads, transcript abundance was normalized by using the RPKM (Reads Per kb per Million reads) method [ 81].
