User: Friederike

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Friederike1.8k
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Genomic Scientist @ Weill Cornell Medical College (Applied Bioinformatics Core)

http://abc.med.cornell.edu/

Posts by Friederike

<prev • 228 results • page 1 of 23 • next >
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Comment: C: How to improve single-cells data ?
... what DNA did you sequence? mammalian? bacterial? ...
written 8 hours ago by Friederike1.8k
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Comment: C: How to improve single-cells data ?
... I don't fully understand the properties of the data set. Is this RNA-seq? If yes, which platform? What types of cells? What exactly do you mean with "10-20% coverage"? ...
written 11 hours ago by Friederike1.8k
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Comment: C: Probabilistic PCA on very sparse SNP matrix
... what's your goal, i.e. what insights do you hope to get from the probabilistic PCA? ...
written 8 days ago by Friederike1.8k
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Answer: A: HTSeq-counts can not map any reads to gtf file
... A typical problem is that the chromosome names don't match between the reference sequence and the GTF file. Try running: ``` samtools idxstats my.bam ``` The output should look something like this: ``` chr1 195471971 1866052 0 chr2 182113224 1667812 0 chr3 160039680 1339058 0 chr4 156508116 1318 ...
written 9 days ago by Friederike1.8k
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Answer: A: Subsetting a RangedSummarizedExperiment in R
... I second everything svlachavas wrote (i.e. following some basic tutorials about R), but in the meantime -- will this do the job? ``` my_subset <- colData(x)$listData head(my_subset) ``` ...
written 9 days ago by Friederike1.8k
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Answer: A: What is the best pipeline step to merge replicates?
... >I saw at Encode they first process the samples independently up to the BAM files, and merge all BAM files using samtools. What would you lose/gain by merging reads at the fastq level? Maybe it's because you still want to know which sample failed the sequencing (if one or several did). That woul ...
written 10 days ago by Friederike1.8k
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Answer: A: What is the best pipeline step to merge replicates?
... >at which point would you recommend merging the reads from multiple replicates When I'm sure that the replicates are sufficiently similar and I have decided that I don't need the information that might be gleaned from treating the replicates independently. As b.nota's comment illustrates: there ...
written 10 days ago by Friederike1.8k
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Answer: A: Low mapping percentage after mapping RNA-seq reads to a closely related species
... >However I wanted to know what other downstream analysis can I do on the reads that actually did map (I'm assuming these would be tRNAs, histones etc) There is no one-size-fits-all solution to the question "what are my genes of interest?". I would probably go about this by pretending you're look ...
written 11 days ago by Friederike1.8k
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Comment: C: Combining multiple files into a single text file in R
... yes, strongly concur with this! I just happened to wrangle with a readMat output recently and they are tricky creatures. The more informatin you can give us about the result of readMat, the more likely we're able to help EDIT: Can you also show the result of reading in just one file (instead of the ...
written 14 days ago by Friederike1.8k
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Comment: C: Finding closest downstream gene including overlap 3' ends
... it'd be easier to help if you had posted your full command(s) including a minimal test set (e.g., three or four genes) ...
written 14 days ago by Friederike1.8k

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Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For A: More than 300.000 peaks for a viral transcription factor - what could this mean?
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
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Scholar 7 weeks ago, created an answer that has been accepted. For A: epigenetic database for immuncells
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Can I use RNA-seq data as control and microarray data as treatment to get differ
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