Exact(8)
The main drawback of BLAT is its poor speed of execution when the set of reads is large.
When the set of reads is large, the aforementioned direct approach to sequence mapping will be very time-consuming.
Regardless of the cause of the difference, our result suggests that when the number of reads is large enough, obtaining subsets from all of the available reads and performing multiple do novo assemblies might be beneficial.
Even if the number of sequenced reads is large, the mapping ratio (the number of mapped reads/the number of sequenced reads) may be poor if the initial amount of DNA is insufficient, for example, because of inefficient ChIP.
There are three main properties of the Illumina Sequence Analyzer output reads that are important to consider: The number of reads is large; one machine run (a single flow cell) generates about 40 million reads in about 48 h.
Although ChIP-seq data contain noise, the probability of H3K4me3 occupying a genome region can be estimated from the sequence reads, as long as the number of reads is large enough for the statistics to be meaningful.
Similar(52)
That is, a pair of reads will be selected if the minimal quality value of the two reads is larger than a given threshold.
In theory, paired-end mapping should mitigate this problem if the gap spanned by the paired reads is larger than the repeat itself.
This was expected considering that BLAT, which was used for soft-clipping realignment, was time-consuming when the set of reads was large.
The numbers of raw data and short reads were larger in developing SASK than in longan [ 23] and peanut [ 15], suggesting that SASK Illumina sequencing could construct a complete read database.
With the capillary technology, each read is large compared to the NG reads.
Write better and faster with AI suggestions while staying true to your unique style.
Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com