Moderator: Ido Tamir

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Ido Tamir4.9k
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Joined:
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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 • 293 results • page 1 of 30 • next >
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Answer: A: Extract overrepresented sequences from fastq or fastqc
... There are many fastqc report parsers written in different languges. E.g. fastqcr for R: library("magrittr") fastqcr::qc_read(fastqc)$overrepresented_sequences %>% dplyr::mutate(name=paste(">",1:n(),"-",Count,sep=""),fa=paste(name,Sequence,sep="\n")) %>% dply ...
written 17 days ago by Ido Tamir4.9k
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Answer: A: How to take out sequences with barcode?
... You could have been more precise with the difference between your read numbers and the stated numbers. If the stated one is bigger in all samples, then its because often and by default demultiplexing is done with 1 mismatch, which grep can not do. ...
written 17 days ago by Ido Tamir4.9k
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Comment: C: RNA-Seq Differential Expression Bash Scripting Error
... I would recommend for a workflow tool. Unless you are already familiar with bash and its a one off analysis its quickly pays off and its not much more difficult than bash. [tutorial][1] . It can work with modules. [1]: https://www.nextflow.io/example1.html ...
written 10 weeks ago by Ido Tamir4.9k
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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 7 months ago by Ido Tamir4.9k
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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 7 months ago by Ido Tamir4.9k
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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 15 months ago by Ido Tamir4.9k
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Comment: C: Paired end vs Single end Differential gene expression analysis
... No. align again only read 1. ...
written 16 months ago by Ido Tamir4.9k
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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 16 months ago by Ido Tamir4.9k
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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 16 months ago by Ido Tamir4.9k
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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 17 months ago by Ido Tamir4.9k

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