User: lien

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lien90
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90
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Belgium
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1 year, 10 months ago
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4 years, 8 months ago
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Posts by lien

<prev • 31 results • page 1 of 4 • next >
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Comment: C: copynumber package in R - basic R question
... Thanks a lot Kevin Blighe and Selenocysteine for all your work! It works perfectly now! ...
written 24 months ago by lien90
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Comment: C: copynumber package in R - basic R question
... Hi I cannot see the resulting plot. But I assume it will look ok. Could you help me out a little bit more on how to use your code? How can I integrate it within the copynumber package in R? Sorry for this probably basic question. ...
written 24 months ago by lien90
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Comment: C: copynumber package in R - basic R question
... I checked the chromosome names and these should be ok: the output was the same when using sort(unique(amut$chr)) and sort(unique(lymphoma.res$chr)). Indeed amut is a data.frame, as well as lymphoma.res. You can find the link to my test file here: https://github.com/Lien-NGSdummie/R-copynumber/is ...
written 24 months ago by lien90
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Comment: C: copynumber package in R - basic R question
... The code doesn't seem too difficult, but still too difficult for me. It seems I still don't understand why it is throwing me this error... > plotFreq function (segments, thres.gain, thres.loss = -thres.gain, pos.unit = "bp", chrom = NULL, layout = c(1, 1), ...) { d ...
written 24 months ago by lien90
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Comment: C: copynumber package in R - basic R question
... Thanks. Great suggestion. Indeed, some columns were not correct (for example factors instead of characters and integer instead of numeric). With the help of 'Google' I managed to convert my input files such that it contains the same columns as the test-dataset. Test-dataset (lymphoma.res): > ...
written 24 months ago by lien90
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copynumber package in R - basic R question
... Hi, I would like to use the plotFreq function that is included in the copynumber package( available via BioConductor in R). I have sequencing data that I converted to a format which I think is the right one for the plotFreq function. The package itself contains a test-dataset called "lymphoma.res" ...
R copynumber plotfreq data input written 24 months ago by lien90 • updated 24 months ago by cpad011212k
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Comment: C: input for Connor: FASTQ files from several lanes
... Thanks but I used the ThruPlex Tag-Seq kit with UMIs and would like to also generate a BAM file with consensus alignment pairs that represent original biological molecules. So I'm afraid Clumpify is not doing everything I need. ...
written 2.2 years ago by lien90
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input for Connor: FASTQ files from several lanes
... Hi all, I would like to use Connor to de-duplicate a tagged BAM file and produce a BAM file with consensus alignment pairs. I used the Thruplex Tag-Seq kit to prepare samples and sequence. However, the sequencing was done on 1 Illumina instrument, but divided over several lanes, resulting in 8 dif ...
fastq bam connor written 2.2 years ago by lien90
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Comment: C: picard metrics without reference file?
... Hi Harold, Thanks for your answer, but I'm not sure it is present in every header. Below the output of samtools view for one of our samples: samtools view -H Part23_sampleA.bam @HD VN:1.4 SO:coordinate @PG ID:Isis PN:Isis VN:2.5.1.3 @SQ SN:M LN:16571 M5:6b9e15a5937653b0006de ...
written 2.8 years ago by lien90 • updated 2.8 years ago by WouterDeCoster41k
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picard metrics without reference file?
... Hi all, For a comparative study, we received BAM-files from a lot of different laboratories. We would like to have a look at the Fold_80_base_penalty and coverage statistics. Therefore, I used the CollectTargetedPcrMetrics part of Picard-metrics. This works fine for the BAM-files that we generated ...
without reference sequence picard written 2.8 years ago by lien90 • updated 2.8 years ago by harold.smith.tarheel4.4k

Latest awards to lien

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