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updated README

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srobb1 committed Nov 1, 2014
2 parents 9b3c89d + aa95893 commit ce3a2066e15f5c14e2887fdf8dce0485e1750e5b
Showing with 625,173 additions and 145 deletions.
  1. +6 −1 README.md
  2. +624,977 −0 sample_relocaTE_run/data/MSUr7.sample.fa
  3. +10 −5 scripts/relocaTE.pl
  4. +12 −3 scripts/relocaTE_align.pl
  5. +144 −116 scripts/relocaTE_insertionFinder.pl
  6. +24 −20 scripts/sam2fq.pl
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@@ -1,4 +1,4 @@
-RelocaTE-1-0-4
+RelocaTE-1-0-5
<A href="http://srobb1.github.com/RelocaTE/">RelocaTE</a>: is a collection of scripts in which short reads (paired or unpaired), a fasta containing the sequences of transposable elements and a reference genome sequence are the input and the output is a series of files containing the locations (relative to the reference genome) of TE insertions in the reference and short reads
1. <strong>non-reference</strong> transposable element insertion events that are present in DNA short read data but absent in the reference genome sequence.
@@ -11,6 +11,11 @@ RelocaTE-1-0-4
<hr>
** Updates **
<hr>
+- 1-0-5:
+ 1. fixed bug: incorrect coordinate positions when using TSD=UNK0
+ 2. added -rr relaxed reference align:allow variable sized fulllen matches of TEs (but must be less than 15kb).
+ 3. allow more relaxed alignment of flankers to reference. Reads that do not map uniquely are now used. Finds more inserts but many may be false positives [option -ra 1]
+ - when -ra 1: "bowtie --sam --sam-nohead --sam-nosq -a -m 1 -v 3" is change to "bowtie --sam --sam-nohead --best -a -v 1"
- 1-0-4:
1. fixed bug: missing existingTE.blatout file.
2. fixed bug: convert fq to fa even when only one file needs to be converted
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