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User: adam.faranda

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adam.faranda • 80
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Posts by adam.faranda

<prev • 21 results • page 1 of 3 • next >
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Why does Hisat2 report a different number of aligned pairs than samtools view?
... Hisat2 reports fewer total aligned reads than `samtools view -F 4 my.alignment.bam`, and I would like to try and understand why. According to my Hisat2 results: 54623054 reads; of these: 54623054 (100.00%) were paired; of these: 30215613 (55.32%) aligned concordantly 0 times ...
samtools rna-seq flags written 3 months ago by adam.faranda • 80
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Comment: C: inner-distance plot created by inner_distance.py is always right-skewed
... Could you clarify what you mean by "from the lab", what procedure did you use to estimate the size distribution of your libraries? I ran inner_distace.py and CollectInsertSizeMetrics on some of my data and the two tools agreed with one another. Both indicated a right skewed size distribution, wit ...
written 3 months ago by adam.faranda • 80
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Choosing between edgeR's exactTest and QLFTest for 2x2 design
... I'm trying to decide whether to use edgeR's QLFTest or ExactTest in a 2 x 2 experimental design. I'm finding that while the two methods largely agree, there are distinct subsets of genes in my data that are only detected by one method or the other. My experiment includes two genotypes (WT and B8 ...
edger rna-seq written 9 months ago by adam.faranda • 80
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How to Interpret FDR-TPR (or FDP-TPR) Curves
... I've seen this type of curve now in several papers benchmarking RNA-Sequencing methods. While they look similar to an ROC curve. There are some cases where the curve takes on an unusual trajectory. ![TPR-FDP Curve][1] Image from:[Van den berge K, Perraudeau F, Soneson C, et al. Observation weig ...
rna-seq written 14 months ago by adam.faranda • 80 • updated 13 months ago by Biostar ♦♦ 20
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Comment: C: RSEM Error - rsem-calculate-expression
... There are a couple of things I can think of. Check your reference directory ../ref/mouse_125; was this file generated when you built the reference? Also -- which aligner are you using, Bowtie/TopHat or STAR ? ...
written 14 months ago by adam.faranda • 80
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Answer: A: HISAT2 Error Building Index
... It turns out the server that I am working on has a Hard Drive Quota of 231 gigabytes per user. I was very close to this quota (226 Gb) in my home directory. I liberated ~ 37Gb of space by deleting some old files, and the indexer now seems to be working properly. I think that the solution here is: ...
written 14 months ago by adam.faranda • 80
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Comment: C: What is the best tool for doing Quality Control checks on my raw RNA-seq data?
... Hi Ana; that is more or less what I am doing. From what I can tell this pipeline is generally considered valid and well accepted. In some pipelines there is a trimming step after running quality control, before running alignments. I've found this to have relatively little impact on my data, but m ...
written 14 months ago by adam.faranda • 80
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Answer: A: What is the best tool for doing Quality Control checks on my raw RNA-seq data?
... I have been using FastQC from the Babraham institute. It is easy to use and gives fairly comprehensive summary statistics. Its output is compatible with multiqc. Multiqc can be used to aggregate several qc reports into a single unified document. FastQC: [https://www.bioinformatics.babraham.ac.uk ...
written 14 months ago by adam.faranda • 80
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HISAT2 Error Building Index
... I consistently get the following error message when I try and build a HISAT2 index for a Mouse geneome. Error: Encountered internal HISAT2 exception (#1) My call to hisat2 is as follows: hisat2-build -f -p 8 --ss genome.ss --exon genome.exon $GENOME genome_tran Where "$GENOME" contains ...
rna-seq hisat2 written 14 months ago by adam.faranda • 80
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What impact does sorting by read name have on RSEM abundance estimates
... The RSEM utility "rsem-calculate-expression" has a setting "--sort-bam-by-read-name". The documentation states that doing so will result in deterministic maximum likelihood estimates, at the cost of longer run-times and larger memory requirements. By default, this setting is disabled Given the sa ...
tools rna-seq rsem written 14 months ago by adam.faranda • 80

Latest awards to adam.faranda

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: What is the best tool for doing Quality Control checks on my raw RNA-seq data?
Scholar 21 months ago, created an answer that has been accepted. For A: Mysterious genes in my Biomart results (genes that were not part of original que
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