User: am

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am20
Reputation:
20
Status:
New User
Location:
European Union
Last seen:
2 days, 12 hours ago
Joined:
6 years, 3 months ago
Email:
a**************@gmail.com

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Posts by am

<prev • 16 results • page 1 of 2 • next >
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Comment: A: How to filter out mouse cells to from a mixture library (mouse and human cells)
... Thank you! https://github.com/10XGenomics/cellranger/issues/24 ...
written 6 weeks ago by am20
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Gini Coefficient and Lorenz curve to measure uniformity of coverage
... Hello, would you suggest me a nice tool to compute Gini index / plot Lorenz curve to estimate uniformity of coverage over the genome other than the R Package ‘ineq’ or the old R Package 'htSeqTools' ? Thank you in advance! ...
gini lorenz curve coverage uniformity written 4 months ago by am20 • updated 11 weeks ago by Biostar ♦♦ 20
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Comment: A: Which is the right bin size for CNV detection in low pass WGS single cell?
... Thank you Igor and Kevin. Yes, the coefficientOfVariation parameter in Control-FREEC allows to automatically determine the correct window size. ...
written 5 months ago by am20
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Comment: C: Which is the right bin size for CNV detection in low pass WGS single cell?
... I'm testing different tools such as CNVkit, Gingko, Control-FREEC... In the CNVkit manual for example I read: "Increase the “target” average bin size (--target-avg-size), e.g. to at least 1000 bases for 30x coverage, or proportionally more for lower-coverage sequencing". I would like to expand thi ...
written 5 months ago by am20
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Which is the right bin size for CNV detection in low pass WGS single cell?
... Hello! I'm performing a single-cell genome-wide copy-number profiling by low-pass sequencing (coverage: 1X, 0.5X, 0.1X). Would anybody suggest me how to determine which is the optimal bin size in the genome segmentation step? Usually it's set to 0.5M or 1M when the genome coverage is as low as 1X. I ...
cnv low pass wgs genome binning single cell written 5 months ago by am20 • updated 5 months ago by Tomás Di Domenico30
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PacBio Long Read error correction through PBcR --> pacbio.spec field
... Hello, I'm trying to self-correct PacBio long fastq sequences using Celera 8.2 assembler through the  PBcR pipeline (http://wgs-assembler.sourceforge.net/wiki/index.php/PBcR). Since the pacbio.spec option is mandatory, can anybody explain me how a correct minimal pacbio.spec file should be built? ...
errorcorrection celera pacbio longreads written 5.7 years ago by am20 • updated 5.6 years ago by geek_y11k
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Comment: C: BWA_MEM on PacBio Reads
... Found it!! Thank you for your time!! ...
written 5.8 years ago by am20
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Comment: C: BWA_MEM on PacBio Reads
... Thank you, this is exactly what I was looking for! Is it explained in the manual? May you give me some references? ...
written 5.8 years ago by am20
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Comment: A: BWA_MEM on PacBio Reads
... Is it possible to cancel a post? Can you teach me how? Thanks! ...
written 5.8 years ago by am20
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Comment: C: BWA_MEM on PacBio Reads
... Thank you Devon Ryan for the reply, i'll delete the one in SeqAnswers :). Do you work with these tools? I would greatly appreciate it if you kindly give me some feedback! I wanted to know how the -x pacbio option works ... originally BWA-mem was not designed with Pac-Bio in mind. I wanted also to n ...
written 5.8 years ago by am20

Latest awards to am

Popular Question 5.7 years ago, created a question with more than 1,000 views. For PacBio Long Read error correction through PBcR --> pacbio.spec field
Popular Question 5.7 years ago, created a question with more than 1,000 views. For BWA_MEM on PacBio Reads
Popular Question 5.7 years ago, created a question with more than 1,000 views. For How To Calculate Overlap Read Lengths

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