From db03ec9a7eaab50dc0303506f8b1c16afddba62e Mon Sep 17 00:00:00 2001 From: Talitha Date: Sun, 9 Aug 2020 22:42:03 -0400 Subject: [PATCH] Update README.rst --- README.rst | 12 +++--------- 1 file changed, 3 insertions(+), 9 deletions(-) diff --git a/README.rst b/README.rst index b78cfc0..1d6e4d2 100644 --- a/README.rst +++ b/README.rst @@ -148,15 +148,9 @@ that reporting a maximum of 100 alignments per read provides an optimal compromi of multi-mappers in many genome builds. However, we highly suggest that users optimize this parameter for their particular experiment, as this could significantly improve the quality of transposable element quantification. -*Optimizing alignment parameters for non-reference strains* - -It is common that the specific laboratory strains used in an experiment contains genomic variations not present in the reference strain. -While this can be mitigated through allowing mismatches during alignments, certain lab strains (e.g. Drosophila melanogaster) have -diverged significantly from the reference genomes. We highly recommend that users should refine their alignment procedures to better -account for the expected variations between their lab strains and the reference genome, which will accordingly improve their analysis -with TElocal. Users can also align to a custom genome build specific to their organism, though they would need GTF annotations for -genes and transposable elements that are compatible with their custom genome in order to utilize TElocal. Please contact us if you -require advice in generating these annotation files. +*Paired end sequencing input* + +For paired-end libraries, it is recommended that only alignments from properly paired reads are present in the input BAM file. I.e., each read 1 alignment should only have a single read 2 alignment. For example, if read 1 matched 3 genomic locations (A, B, C), then if read 2 also match 3 genomic locations (A', B', C'), then all three pairs of alignments could be used (and should be in the BAM file). However, if alignment C of read 1 was matched with more than one alignment of read 2 (e.g. C' and C*), then alignment C should be discarded (as there are unmatched alignments between read 1 and read 2). `STAR `_ only outputs properly paired alignments by default, while `Bowtie2 `_ requires the :code:`--no-mixed` parameter to be used. *Specific recommendations when using STAR*