User: biobiu

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biobiu90
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Posts by biobiu

<prev • 26 results • page 1 of 3 • next >
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Prediction of genes and functions without reference genome
... Hi, I plan to sequence the genome of un-referenced bacteria. My first goal is to try to define functional elements in the genome and next to predict their function. My general idea is to assemble the reads into contigs, perform ORF calling, blast genes against DBs, translate the genes into proteins ...
assembly written 6 weeks ago by biobiu90 • updated 6 weeks ago by proteina.cbe0
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Comment: C: CNVkit- weird results when using the same sample as normal
... Thanks for your reply, I'll clarify. There are no two commands, just a batch command of the same sample as test and normal sample: cnvkit.py batch SAMPLE.bam -n SAMPLE.bam --targets TAR.bed --annotate refFlat.txt --fasta ~ucsc.hg19.fasta --access access-5k-mappable.hg19.bed --output-reference re ...
written 11 weeks ago by biobiu90
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CNVkit- weird results when using the same sample as normal
... Hi, I'm using CNVkit to detect copy number alterations in hybridized capture panel. When I've used the same sample (exactly the same bam) as a reference I somehow do find some CNA. We used the batch command followed by the call command with default parameters (and with dropping low-coverage). 15 out ...
cnv written 12 weeks ago by biobiu90 • updated 11 weeks ago by Eric T.2.5k
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Answer: A: Pearson's Correlation Coefficient and expression matrix
... Use the function [cor][1] in R. You have a good example [here][2]. [1]: https://www.rdocumentation.org/packages/stats/versions/3.5.3/topics/cor [2]: http://www.sthda.com/english/wiki/correlation-matrix-a-quick-start-guide-to-analyze-format-and-visualize-a-correlation-matrix-using-r-software ...
written 3 months ago by biobiu90
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Comment: C: extract some feature from peak?
... you may use some tools in bedtools suite- intersecting the bam with the intervals bed file by **intersectBed**, use **coverage** to compute depth and breadth, and even genomecov and an in house script. ...
written 3 months ago by biobiu90
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treating out-of-range values
... Hey, I have some metabolites data. However, in several samples and metabolites the values are out-of-range. The nice things is that the I can distinguish between values below and above the range. How would you treat these values? some options that I were thinking about 1) Assign these values as N ...
brainstorm written 3 months ago by biobiu90
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Answer: A: miRNA differential expression
... I agree with ATpoint- there is no easy answer for which of them is better. Two additional comments: 1) It is highly important to do pre-processing for miRNA-seq reads (removing adapters, low-quality sequences, size enrichment). 2) As for the alignment- there are several aligners and methods the ca ...
written 3 months ago by biobiu90
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Comment: C: CNVkit: Dealing with noisy tumor samples
... Dear Eric, Did you had a chance to check the performance of CNVkit with pooled tumor samples? We have targeted, hybrid capture, sequencing data and have no normal samples. I'm wondering which of the following setups, in principal, should be preferred: 1) Calling CNVs with no control samples (a f ...
written 3 months ago by biobiu90
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Comment: C: Panel of tumors for CNV detection
... Following further reading- I think I'll try to use CNVkit, gatk and copywriteR. Did anyone tried these tools with such "panel of tumors"? or know which should be less sensitive for this kind of input? ...
written 3 months ago by biobiu90
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Answer: A: Have you ever obtained user guide of ExomeCNV?
... http://www2.uaem.mx/r-mirror/web/packages/ExomeCNV/ExomeCNV.pdf and here is the CRAN archive: https://cran.r-project.org/src/contrib/Archive/ExomeCNV/ ...
written 3 months ago by biobiu90

Latest awards to biobiu

Popular Question 8 weeks ago, created a question with more than 1,000 views. For Does mirna-seq is stranded?
Popular Question 3 months ago, created a question with more than 1,000 views. For Uniquly aligned reads by BWA-mem (MAPQ, and XA tag)

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