Moderator: Ido Tamir

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Ido Tamir4.9k
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i********@imp.ac.at

Tired of missing provenance for your fastq files?

Not knowing which scales the qualities are on?

 

Handling two files for paired end reads instead of one?

 

 

Try bam files instead! A well defined specification (for biological standards). Easy to use tools.

 

Convert illumina basecalls to bam files fresh from the machine: illumina2bam https://github.com/gq1/illumina2bam

 

Posts by Ido Tamir

<prev • 290 results • page 1 of 29 • next >
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Answer: A: FastQC:"Per Base Sequence Quality"
... These are boxplots where the box normally covers the interquartile range i.e. 25%-75%. The wiskers are convention and in fastqc according to the docs 1,9.th decile. Then you have mean and median indicated. The background coloring is of course arbitrary where they say a value below 20 is bad "red" a ...
written 5 weeks ago by Ido Tamir4.9k
0
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Answer: A: ggplot: adjust X ticks positions in boxplots
... 1. this is not bioinformatics, but ggplot for which there are other forums e.g. stackoverflow 2. wherever you post, you should add some way that people can reproduce this easily in a code script with e.g. random data, and not download data from some wierd site. 3. From your data.csv I have the im ...
written 6 weeks ago by Ido Tamir4.9k
2
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Answer: A: Markduplicates in RNASEQ
... Duplication measures the amount by which one read (sequence) is present multiple times. Uniquely mapping / multiple mapping concerns the times one read (sequence) is present in the genome (transcriptome). Both are independent of each other: A duplicated read can map to one region or multiple regions ...
written 9 months ago by Ido Tamir4.9k
2
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Comment: C: Paired end vs Single end Differential gene expression analysis
... No. align again only read 1. ...
written 10 months ago by Ido Tamir4.9k
0
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Comment: C: Paired end vs Single end Differential gene expression analysis
... I don't understand the question. Please explain in steps what you want to do and how it differs from what I described above. ...
written 10 months ago by Ido Tamir4.9k
1
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Answer: A: Paired end vs Single end Differential gene expression analysis
... The best thing you can do is to disregard the 2. read, trimm them to the same length from the 3' end and align only the 1. read. Look at technical parameters errors/cycle, coverage across genes, etc ... per group to ensure that differences are probably mostly biological. Most of the times the runs h ...
written 10 months ago by Ido Tamir4.9k
1
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1
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Comment: C: RNA-seq amending fasta/fastq files (from one line into two lines)
... please reformat the examples. everything is just one line. also its length($4) == 22 and in awk you can also test for G at 5' ...
written 11 months ago by Ido Tamir4.9k
1
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Comment: C: BWA -> samtools pipe while filtering mapped & unmapped reads
... have a look at e.g. [nextflow][1] it will pay off after some learning as soon as the workflow gets more complex [1]: http://nextflow.io ...
written 12 months ago by Ido Tamir4.9k
1
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Answer: A: ggplot expression values as function of samples and classes
... Then add a column sample to "reduced_data" then library("reshape2") m <- melt(reduced_data, id.vars=c("samples","class"), variable.name=("miRNA")) ggplot(m, aes(x=samples,y=value,colour=miRNA))+ facet_grid(. ~ class) In general in ggplot2 its always bringing the data into the corr ...
written 13 months ago by Ido Tamir4.9k
0
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534
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Comment: C: wrong bam file format
... do `grep '>' genome.fa` Also: the headers you have now look like from transcripts. The second column is the length of the contig. If you have additional chromosomes, UCSC does not care. It only cares if it cant find the one it wants to display in your bam file. Please write the UCSC error into t ...
written 13 months ago by Ido Tamir4.9k

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