Tweet
Hi,
Anyone know of a tool which does soft adapter clipping, quality trimming of unaligned reads in .bam format?
Thanks
Anyone know of a tool which does soft adapter clipping, quality trimming of unaligned reads in .bam format?
Thanks
-
-
Not that I know of, but as a workaround, you could convert to fastq and then use Trimmomatic or FastX.Originally posted by mehc View Post -
These won't do soft clipping, however; you'd have to parse their output and do some wild guesswork on the clippings. I would rather take the source and make a fork instead which outputs soft-clipped SAM/BAM.Originally posted by pbluescript View Post
@mehc: Do you have an aligner or assembler which accepts soft-clipped bases in a BAM as input? I haven't had that yet (for Illumina data). I've seen aligners soft-clipping bases in the output alignments, however. Or are you writing something on your own and would like to use such information?Comment
-
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...05-06-2024, 07:48 AM -
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM
Comment