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STAR aligner cant map too short reads - Biostar: S For our Ribo-seq data set I tried the star aligner but was able to map only a very small fraction of the reads (<1% in some samples), while most of the reads a discarded for being too short
Samtools flagstat 0% properly paired - SEQanswers I'm quite confused, as I have nearly 91% of my reads mapping to my reference, but barely any properly pairing QC analysis (using FastQC) did not show anything out of the ordinary, and the library prep gives an average fragment that we are used to seeing
RSeQC: An RNA-seq Quality Control Package — RSeQC documentation Two strategies were used to determine reads duplication rate: * Sequence based: reads with identical sequence are regarded as duplicated reads * Mapping based: reads mapped to the exactly same genomic location are regarded as duplicated reads
flagstats results show 0. 0 % properly paired reads In any case, it's odd that 0 reads are paired I would expect there to be a few just by random chance out of 75 million (though that depends on the genome size)
Trimmomatic Paired End - Low number of surviving reads If this is a re-sequencing project you shouldn't worry about trimming based on Q-scores But the problem is that I need paired files for my analysis and there are only 66% reads surviving in pair Any suggestion on how to improve the number of surviving reads in both forward and reverse?
Low % of properly paired reads · Issue #125 · amplab snap - GitHub The current version of SNAP won’t do this It only soft clips where it’s supposed to do so based on the base call quality string So, only half of the reads align, and so only about a quarter of the pairs have both halves aligning