User: madk00k
madk00k • 340
- Reputation:
- 340
- Status:
- Trusted
- Location:
- Heidelberg
- Website:
- http://okko73313.blogs...
- Last seen:
- 1 year, 6 months ago
- Joined:
- 7 years, 8 months ago
- Email:
- o********@gmail.com
Bioinformatics researcher with passion to discover new things.
Posts by madk00k
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... Thanks for reply! I will check these papers for sure ...
written 3.6 years ago by
madk00k • 340
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... 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 3.6 years ago by
madk00k • 340
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... 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 ...
written 3.6 years ago by
madk00k • 340
• updated
3.6 years ago by
Shicheng Guo • 7.8k
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... 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 4.2 years ago by
madk00k • 340
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... 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 ...
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... Qualimap computes coverage and many other QC issues from BAM file. Here's the link:
http://qualimap.bioinfo.cipf.es/
...
written 4.4 years ago by
madk00k • 340
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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 4.7 years ago by
madk00k • 340
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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 4.8 years ago by
madk00k • 340
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... 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 4.8 years ago by
madk00k • 340
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... Tnx, hopefully it will be useful for ppl who work on this topic
...
written 5.2 years ago by
madk00k • 340
Latest awards to madk00k
Popular Question
3.4 years ago,
created a question with more than 1,000 views.
For Single cell RNA-seq with ERCC spike-ins: appropriate normalization methods for cell types investigation
Teacher
3.4 years ago,
created an answer with at least 3 up-votes.
For A: Estimate Insert Size In Paired-End/Mate-Pair
Appreciated
6.2 years ago,
created a post with more than 5 votes.
For A: Resources For Learning How To Deal With Next Generation Sequence?
Good Answer
6.2 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
6.2 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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