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Another assembly-independent reason is the lack of reads in the library for these regions.
Downstream of pXO1_0138 is a gap where the lack of reads is evident, suggesting termination of the mRNA for genes pXO1_0138, pXO1_0139, and pXO1_0140 at this location.
To investigate the lack of reads further, PCR amplification using primers designed to amplify exon 6, plus 50 bp of flanking intron, was performed.
SNP genotyping revealed a region on chromosome 4 shared by all affected individuals and whole-exome sequencing showed a lack of reads across AMBN exon 6.
In the post-ZGA transcriptome, the lack of reads supporting usage of promoter 1 demonstrates degradation of the maternal-specific 5' distal isoform during the MBT.
The additional 3 transcripts and 9 proteins that were not found at the final stage were due to reasons seen previously, lack of reads or longer irrelevant open reading frames, respectively.
Similar(50)
Alignment of reads against reference genome HG19 was performed using TopHat and analyzed using Cufflinks.
Coverage of reads is shown on the upper part of the IGV image.
(b) Coverage of reads by formaldehyde-assisted isolation of regulatory elements (FAIRE).
Number of reads, % of unique and duplicated reads and resulted mean coverages are reported.
d Number of reads that could not be mapped to the assembled pseudomolecules.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com