Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.
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If you'are using "bwa sampe" for aligning, the documentation says:
I don't know if it is the case with "bwa mem" or with "bwa aln". -
#1 = Unless there is/are SNP's which are captured by that particular read you would not be able to tell where the read came from. I assume the sequence of the gene is otherwise identical?Leave a comment:
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Deciding how many reads map to a plasmid or to a genome
Hi all,
I have illumina genome reads for an E. coli a collaborator is studying. The prep used had a plasmid as well. I have two questions:
1) For the reads that match both (e.g. lacI gene), how can I tell which came from the plasmid and which came from the genome?
2) Should I normalize by dividing on the total reads per library or only the mapped reads in a library?
Thanks in advance...Last edited by fznajar; 01-09-2019, 01:44 PM.
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Ribonucleic acid (RNA) represents a range of diverse molecules that play a crucial role in many cellular processes. From serving as a protein template to regulating genes, the complex processes involving RNA make it a focal point of study for many scientists. This article will spotlight various methods scientists have developed to investigate different RNA subtypes and the broader transcriptome.
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