User: lieven.sterck

gravatar for lieven.sterck
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Belgium, Ghent, VIB
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Posts by lieven.sterck

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Assembly with mate-pairs issue
... Hi Shaun, OK, this works perfectly as expected! before I close this thread as resolved, one small additional question. You mention (or recommend) to concatenate all the data from a single lib (potentially from multiple lanes) into a single input file. Can you elaborate on why? Is it a technical rea ...
written 10 hours ago by lieven.sterck20
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Comment: C: Assembly with mate-pairs issue
... Thx for the reply. ah, good question, I'll check (if I have access to that kind of detailed info) . This is nonetheless only a subset of my total input data (doing this currently to optimise kmer etc and to test protocol). I certainly have mate pair data of diff libs (and to some extent also for t ...
written 4 days ago by lieven.sterck20
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Comment: C: Assembly with mate-pairs issue
... Here is the one for the run with the MP data: abyss-pe np=50 -C k$1 name=ppinTk$1 k=$1 \ lib='D1MNAACXX_2 D1MNAACXX_3 D1MNAACXX_6 D1MNAACXX_7 D1MNAACXX_8' \ mp='C1MLEACXX_3 C1MLEACXX_4' \ D1MNAACXX_2="$inDIR/D1MNAACXX_2_0_1.cleanTrim.fq.gz $inDIR/D1MNAACXX_2_0_2.cleanTrim.fq.gz" D1M ...
written 5 days ago by lieven.sterck20
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Answer: A: Solanum tuberosum reference, where can I download it?
... Or via the download link on this page: http://bioinformatics.psb.ugent.be/orcae/overview/Soltu ...
written 17 months ago by lieven.sterck20
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Comment: C: Help Interpreting Abyss-pe Character Occurrence Table
... Thx for resolving this Ben. One related question: is it correct to assume then that it are mainly the reads from the 'different' category that will contribute to the contig and scaffold building stage? ...
written 19 months ago by lieven.sterck20
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Comment: C: Help Interpreting Abyss-pe Character Occurrence Table
... I agree with most of this but I'm not sure on your explanation for 'singleton'. ABySS uses the aligned pairs to build a distribution of insert sizes so, to me it would not make much sense to already limit the mapping to an expected insert size. I therefore think that singleton is only pointing to th ...
written 19 months ago by lieven.sterck20
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Comment: C: Abyss assembler mapping
... Hi Ben, I had a similar setup as Damian in mind so your comment greatly helped me too. Indeed pre-building the indexes somewhat reduces runtime for the abyss-map step (I have to align 50+ libraries so in the end that saved me quite some time). Related: I'm actually wondering if there is any advant ...
written 21 months ago by lieven.sterck20
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Assembly with mate-pairs issue
... hi, I'm conducted an assembly of a genome and during the testing phase (different inputs, K-mer and such) I made an observation that worries me a little. here is the situation: I have 2 assembly results using the same paired and single end read input data set but in one of them I added additional m ...
assembly abyss mate-pairs written 21 months ago by lieven.sterck20 • updated 4 days ago by Shaun Jackman360
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Comment: C: readlink error when using abyss-dida aligner
... Thx for this fix! I came up myself with a similar patch but yours is cleaner ;-) ...
written 22 months ago by lieven.sterck20
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readlink error when using abyss-dida aligner
... I'm running an assembly with abyss and I wanted to give this new distributed aligner option DIDA a try. Unfortunately it did not ran successfully and I was reported the following error: readlink: extra operand `/CleanOK/C1MLEACXX_3_0_2.cleanTrim.fq.gz' Try `readlink --help' for more informa ...
dida assembly abyss written 22 months ago by lieven.sterck20 • updated 22 months ago by benv620

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