Thanks for your help. I have added examples in the question.
• 0 views
•
link
written
by
chjiao3456 •
Tools to remove duplicate or substring reads
Is there any efficient tool to remove substring reads or duplicate reads from NGS data set? I know that readjoiner could remove the duplicated reads, but seems not work on substring reads. Thanks.
Example: Duplicates: read1: AGTCAT read2: AGTCAT In this case, only one read will be kept.
Substring: read1: GTCA read2: AGTCAT In this case, read1 will be removed.
• 2,021 views
•
link
written
by
chjiao3456 •
2 answers
The most efficient tool for this purpose is Dedupe from the BBMap package. However, it requires all reads to be stored in memory, so it needs a lot of memory. Can you explain in more detail what you are trying to do?
• 0 views
•
link
written
by
Brian Bushnell
Just noticed that SGA tool is able to do this. Collapse Reads That Are Substrings Of Other Reads In Same Library
• 0 views
•
link
written
by
chjiao3456 •
Log in to answer this question.
More posts like this
-
Table summary for SNP linkages from same read
written by noodle
-
how to handle duplicate reads in unpaired Whole Exome Sequence
written by adR
-
Remove duplicate reads for bisulfite sequencing reads
written by qwzhang0601
-
Demultiplexing and deduplicating using barcodes and UMIs in the "mate" read
written by lech.kaczmarczyk •
-
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
written by chen
-
Samtools rmdup and Piccard Markduplicates
written by Prakash
-
Remove Duplicate Reads from paired end data set
written by Tonor
-
Picard vs Samtools duplicate removal
written by conorproud89 •
-
Where to find PCR duplicate reads in bam file?
written by bioinforesearchquestions
-
Adapter for RNA-seq alignment
written by chjiao3456 •
