User: Veranja Liyanapathirana

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4 years, 9 months ago
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Posts by Veranja Liyanapathirana

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Barcode Splitter On Paired End Illumina Reads
... Dear Galaxy team   I am so sorry for repeatedly posting the same question, but I do need some inputs in to this.   Please let mek now the best way to use barcode splitter on Paired end Miseq data. The data is already split for the Illumina indexes using Miseq reporter, what I want to do is to split ...
galaxy written 4.8 years ago by Veranja Liyanapathirana70 • updated 4.7 years ago by Jennifer Hillman Jackson23k
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Barcode Splitter On Paired End Reads
... Dear Galaxy team,   I am sorry for repeatedly asking this question but I would like some feed back from anyone who has used barcode splitter on paired end reads as the different alternatives I used do not give satisfactory results in terms of expected read alignments. I have a set of Illumina Miseq ...
bowtie alignment written 4.8 years ago by Veranja Liyanapathirana70
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Prolonged - Job Waiting To Run
... Dear Galaxy team,   I am running short read alignments with Bowtie for illumina using some data generated from split data using barcode splitter. The alignment programme has been indicated the "job waiting to run" status for nearly over an hour. I can meanwhile perform other functions such as data u ...
bowtie alignment written 4.8 years ago by Veranja Liyanapathirana70 • updated 4.8 years ago by Jennifer Hillman Jackson23k
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Comment: C: Using Segments Of Sequences As A Reference Genome - Bowtie For Illumina
... Dear Dr. Jennifer,   Thank you very much for the reply. I am sorry about the way the thread was handled. Your input is much helpful. However, I have one key question which probably didnt come across well in the third question and I will try to re-word it. I am using Illumina paired end data and need ...
written 4.8 years ago by Veranja Liyanapathirana70
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Comment: C: Using Segments Of Sequences As A Reference Genome - Bowtie For Illumina
... Dear all,   I was using the barcode splitter on Miseq paired end reads, however I am not sure if I did it correctly as the results I get in terms of the number of reads alocated per each barcode does not tally with the resutls obtained by the our service provider by one of their in-house script base ...
written 4.8 years ago by Veranja Liyanapathirana70
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Answer: A: Using Segments Of Sequences As A Reference Genome - Bowtie For Illumina
... Dear Galaxy team/ users,   I am sorry to spam the thread again but I still could not figure out what is worng with my work flow and need some help.   As mentioned earlier, I use Miseq reads, demultiplex for an inhouse barcode using barcode splitter, re-upload and map with a ref sequence that is cons ...
written 4.8 years ago by Veranja Liyanapathirana70
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Using Segments Of Sequences As A Reference Genome - Bowtie For Illumina
... Dear all, My problem seems like something that should have a very simple solution from my end and due to my lack of knowledge in bioinformatics, I am probably messing up with the workflows. The experiment I run is one where we used Miseq to sequence amplicons of a multiplex PCR. We introduced an inh ...
bowtie alignment written 4.8 years ago by Veranja Liyanapathirana70

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