Moderator: Ido Tamir

gravatar for Ido Tamir
Ido Tamir4.8k
Reputation:
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Location:
Austria
Last seen:
4 months, 2 weeks ago
Joined:
7 years ago
Email:
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 • 288 results • page 1 of 29 • next >
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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 7 months ago by Ido Tamir4.8k
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Comment: C: Paired end vs Single end Differential gene expression analysis
... No. align again only read 1. ...
written 8 months ago by Ido Tamir4.8k
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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 9 months ago by Ido Tamir4.8k
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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 9 months ago by Ido Tamir4.8k
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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 9 months ago by Ido Tamir4.8k
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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 10 months ago by Ido Tamir4.8k
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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 11 months ago by Ido Tamir4.8k
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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 11 months ago by Ido Tamir4.8k
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Answer: A: wrong bam file format
... Because you aligned to the transcriptome. With tophat you align to the genome + a transcriptome annotation in GTF format if you have one at hand. And check the names of the chromosomes. ENSEMBL does not do the chr prefix. You might have to change it in the files. ...
written 11 months ago by Ido Tamir4.8k
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Comment: C: How to convert TPM to raw reads
... for TPM you divide (among other things) by the total number of reads. This info is lost. In addition to this you also normalize by something like 'effective exon length' and you would need to know how the person/program actually calculated this, which reference was used etc. This will not work. St ...
written 13 months ago by Ido Tamir4.8k

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Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Popular Question 9 months ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Appreciated 9 months ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
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Scholar 11 months ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
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Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Scholar 15 months ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
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