User: eddreuzy

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eddreuzy0
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Posts by eddreuzy

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Answer: A: Troubles with full settings on Lastz
... Thank you very much for that detailed answer, I did see the existence of the --noytrim option in the command line Lastz and could not find it on Galaxy.. I will try to find another way around by reducing the query coverage as you advised, Ed   ...
written 2.5 years ago by eddreuzy0
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Answer: A: Troubles with full settings on Lastz
... Ok, just to say that I found out how to trim each read to the right position.  (I will split the file in multiple files, each one for a particular lentgh, perform the trimming and pool together the trimmed sequences) Edouiard ...
written 2.5 years ago by eddreuzy0
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Answer: A: Troubles with full settings on Lastz
... Hi, Thank you for that help! Sorry, I realized that what I wrote was not very clear, Here is the context : I want to map viral insertion sites in the genome. to that aim, I amplify vector -genome junctions by PCR. Therefore I end up with reads containing a 39nt sequence corresponding to the 3' en ...
written 2.5 years ago by eddreuzy0
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Troubles with full settings on Lastz
... Hi, I am new to bioinformatics and I have troubles using Lastz. I use it to detect a 39nt sequences at the beginning of the reads. I want to keep all reads with no more than 3mismatch/39nt and 1gap/insertion. I had good results using yasra setting "454 75%homology" and filtering for 90%homology ...
galaxy alignment lastz written 2.5 years ago by eddreuzy0 • updated 2.5 years ago by Bob Harris190
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Trimming sequences with homology parameters
... Hello, I am processing single-end illumina reads coming from a PCR library.  I know the flanking sequences of my reads and need to:  - select the sequence that contain the 5' constant region (with >90%homology for the 39 first nt; 100% for the last 3nt) and remove that sequence - remove the 3 ...
trimming galaxy written 2.5 years ago by eddreuzy0
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FlexBar output appears only as txt ?! I can not use it in worflows ?
... Hello, I am using Flexbar on the CRS4 Orione galaxy server. This tool is very useful as it allows to define homology parameters for barcode detection/removal and adapter removal. The problem is : when I add it to my workflow it is impossible to connect it with the downstream steps !! I realized tha ...
galaxy software error written 2.5 years ago by eddreuzy0 • updated 2.5 years ago by Jennifer Hillman Jackson23k

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