User: madk00k

gravatar for madk00k
madk00k330
Reputation:
330
Status:
Trusted
Location:
Heidelberg
Website:
http://okko73313.blogs...
Last seen:
10 months, 1 week ago
Joined:
6 years, 11 months ago
Email:
o********@gmail.com

Bioinformatics researcher with passion to discover new things.

Posts by madk00k

<prev • 25 results • page 1 of 3 • next >
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Comment: C: Single cell RNA-seq with ERCC spike-ins: appropriate normalization methods for c
... Thanks for reply! I will check these papers for sure ...
written 2.9 years ago by madk00k330
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Comment: C: Single cell RNA-seq with ERCC spike-ins: appropriate normalization methods for c
... Actually the spike-ins are there. I did not perform initially the alignment to ERCC references, only to normal reference, now this is fixed. ...
written 2.9 years ago by madk00k330
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Single cell RNA-seq with ERCC spike-ins: appropriate normalization methods for cell types investigation
... I am working on scRNA-seq data generated using ERCC spike-in. Main goal is to investigate the cell types and perform special clustering. I have only have access to the formed fastq files without spikes. Each Fastq file belongs to a certain cell. My question is the following: is the FPKM normalizatio ...
scrna-seq normalization written 2.9 years ago by madk00k330 • updated 2.9 years ago by Shicheng Guo7.4k
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Comment: C: Rseqqc And Rna-Seqqc - Quality Control Software For Rna-Seq Data
... Both tools are quite good and useful, however there are currently some novel applications available, which provide additional important quality control checks. For example, Qualimap is an open-source Java program, which includes several modes to analyze QC of high throughput sequencing alignment dat ...
written 3.5 years ago by madk00k330
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Answer: A: Which software do you use for RNA-seq data quality control?
... A novel version of open-source Qualimap tool provides additional aspects specific to RNA-seq data quality control analysis. Most importantly, now multi-sample data analysis is supported providing abilities to detect outliers. Here's a link to publication which includes detailed comparison of Qualima ...
written 3.5 years ago by madk00k330
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Answer: A: Qc And Coverage From Paired-End Reads
... Qualimap computes coverage and many other QC issues from BAM file. Here's the link: http://qualimap.bioinfo.cipf.es/ ...
written 3.7 years ago by madk00k330
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Answer: A: alignment summary from tophat
... Try using QualiMap to analyze the resulting alignment. There are 2 modes possible: RNA-seq QC or BAM QC with GTF file. ...
written 4.0 years ago by madk00k330
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Comment: C: Adding Read Groups To Bam Files
... Now this link is not working, but this one does: http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups ...
written 4.1 years ago by madk00k330
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Answer: A: Count Junctions In A Sam/Bam File
... New version of Qualimap tool counts junctions in RNA-seq Quality Control mode. QualiMap can downloaded from here. Here's an example of report. ...
written 4.1 years ago by madk00k330
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Comment: C: Which Multiscale Genome Browser Is The Best At Visualizing Structural Variants?
... Tnx, hopefully it will be useful for ppl who work on this topic ...
written 4.5 years ago by madk00k330

Latest awards to madk00k

Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Estimate Insert Size In Paired-End/Mate-Pair
Appreciated 5.5 years ago, created a post with more than 5 votes. For A: Resources For Learning How To Deal With Next Generation Sequence?
Good Answer 5.5 years ago, created an answer that was upvoted at least 5 times. For A: Resources For Learning How To Deal With Next Generation Sequence?
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Resources For Learning How To Deal With Next Generation Sequence?

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