Moderator: igor

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igor8.8k
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Posts by igor

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Comment: C: Getting uniquely aligned properly paired reads
... And if so, what is the problem with the VCF that it generates? ...
written 21 minutes ago by igor8.8k
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Comment: C: ERROR running annovar with cosmic90
... It should be: `sed 's/GENOMIC_MUTATION_ID/Mutation ID/'` (without `<` or `>`) ...
written 9 days ago by igor8.8k
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Comment: C: fastest UMAP method
... To clarify, the suggestion was to experiment with different parameters using a small subset. Then apply the optimal settings to the full dataset. That will answer the question of how representative the subset was. I personally would be curious to see an example using real biological data with over ...
written 9 days ago by igor8.8k
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Comment: C: fastest UMAP method
... You can also subset your data for exploratory analysis. I would argue that after 50,000 points, you won't really be able to see any differences anyway. There are only so many dots you can put on a plot before they simply start overlapping the previous dots. ...
written 10 days ago by igor8.8k
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Answer: A: fastest UMAP method
... If speed is a concern, you can perform PCA prior to UMAP, reducing your input matrix. Many single-cell packages do that by default, so it's a fairly common practice. You can read previous discussion here: https://www.biostars.org/p/381993/ To speed up the PCA computation, you can use the [irlba][1] ...
written 12 days ago by igor8.8k
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Comment: C: ATAC-seq pipeline check to remove RF reads
... I am not sure there is any problem with the data based on that plot alone. If your fragments are shorter than your reads, Bowtie would consider those discordant. If you change the Bowtie settings or trim the reads, that would change how the reads are classified. ...
written 15 days ago by igor8.8k
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Comment: C: ATAC-seq pipeline check to remove RF reads
... Have you seen this previous extensive discussion? https://www.biostars.org/p/387531/ ...
written 15 days ago by igor8.8k
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Comment: C: trim galore for 10Xgenomics
... 10x provides extensive documentation on how to run Supernova: https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/using/fastq-input ...
written 17 days ago by igor8.8k
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Comment: C: Finding FASTQ files for TCGA Data
... As you already answered yourself, FASTQs are controlled access. ...
written 17 days ago by igor8.8k
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Comment: C: trim galore for 10Xgenomics
... I would try Supernova first to see what you get. That would serve as a good control. If you use Trim Galore and Abyss, you skip generation of linked (long) reads, which is the benefit of 10x Genomics technology over standard short-read sequencing. ...
written 17 days ago by igor8.8k

Latest awards to igor

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Popular Question 5 days ago, created a question with more than 1,000 views. For TCGA sample names for .idat files
Popular Question 8 days ago, created a question with more than 1,000 views. For TCGA sample names for .idat files
Appreciated 13 days ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Good Answer 18 days ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Great Question 21 days ago, created a question with more than 5,000 views. For Faster BLAST alternative
Scholar 24 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Scholar 5 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
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Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Best Program to use for DE Analysis
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Scholar 9 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: .bam files to fastq including the unmapped reads
Scholar 11 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
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