User: lait

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lait140
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Posts by lait

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number of cycles, Nextseq500, for whole exoems equencing, which option is more efficient?
... Hi all, we are moving from Illumina Hiseq2500 to Nextseq500 soon. For our Hiseq2500 we had reads of 101 bp length. We mainly use it for whole exome sequencing, and we have a well established pipeline for the full analysis of the WES data. **-1-** - With respect to Nextseq500, my question is: co ...
nextseq hiseq cycles reads-length written 9 weeks ago by lait140 • updated 9 weeks ago by toralmanvar820
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Comment: C: EXCAVATOR shows 1 deletion which is not TRUE in IGV
... The coverage of the gene is almost the same acrross the other exons.. EXCAVATOR shows a genotype of 1/1 for that deletion.. actually it shows a genotype of 1/1 for all the detected CNVs, whether it is a deletion or an insertion. Do you recommend another good SV caller for exome data to try if the re ...
written 5 months ago by lait140
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EXCAVATOR shows 1 deletion which is not TRUE in IGV
... Hi, I have WES data for a sample having a specific phenotype. I ran EXCAVATOR on that sample, trying to detect CNVs. I am interested to check deletions happening on gene A, because patients having that specific phenotype would frequently get deletions in that gene A. In EXCAVATOR's results file: ...
exome excavator wes cnv igv written 5 months ago by lait140
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bionano's raw data of images, safe to delete?
... Hi everyone, this question is for those who have worked with bionanogenomics data. Do you think the raw data, which is basically images of points, which are used to produce the molecules, is of any use? each run generates around 1 TB of raw data, and I would like to know if this data would be of an ...
rawdata bionano molecules written 5 months ago by lait140
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Comment: C: bionano hybrid scaffold
... thanks for your answer, that is correct. but do you think WES data could be in any way useful , as a complementary data, for the bionano optical mapping? ...
written 5 months ago by lait140
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bionano hybrid scaffold
... Hi, is it possible to use illumina whole exome sequencing data as input for the hybrid scaffold tool in bionano access software ? I have WES data and bionano assembly data for the same sample. I was wondering if the WES data is enough to be used by the hybrid scaffold tool? Thanks ...
optical mapping wes bionano illumina written 5 months ago by lait140 • updated 5 months ago by WouterDeCoster41k
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Comment: C: tool to detect large deletions
... thanks, already edited the question. ...
written 6 months ago by lait140
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tool to detect large deletions
... Hi, I used to look for large deletions in IGV, but is anyone familiar with a tool that could detect large deletions, (for example, deletions of 4 exons in a certain gene) effectively and automatically ? any recommendations ? edit: I am looking for those big deletions in around 300 genes only, so ...
deletions wes igv written 6 months ago by lait140 • updated 6 months ago by bari.ballew190
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putative mosaic mutations
... Hi, I have trio WES data for mothers, fathers and children with cancer. I have detected potential denovo mutations in children using varscan trio mode. I am looking now for potential mosaic mutations in the child, Can I consider the denovo mutations with AF < 0.3 in the child and AF = 0 in bot ...
mosaic de novo wes sequencing written 7 months ago by lait140
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Comment: C: find coverage of specific exomes from a bam file
... ASCII text and the second command returned nothing So in my case, the start and end coordinates are equal, I dont know why the condition turned to be TRUE ...
written 11 months ago by lait140

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