Moderator: Ido Tamir

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Ido Tamir4.8k
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Location:
Austria
Last seen:
1 day, 17 hours ago
Joined:
6 years, 4 months 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 • 287 results • page 1 of 29 • next >
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Comment: C: Paired end vs Single end Differential gene expression analysis
... No. align again only read 1. ...
written 28 days 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 4 weeks 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 4 weeks 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 6 weeks 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 12 weeks 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 3 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 3 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 3 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 5 months ago by Ido Tamir4.8k
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Answer: A: FPKM vs READ COUNT
... I suspect either a rounding error (but you have others with less counts that show FPKM) or maybe the annotation is wrong or wrongly formatted. If possible let the tool (which one are you using?) also output the length of the gene/transcript. Maybe one exon spans a whole chromosome or something simil ...
written 5 months ago by Ido Tamir4.8k

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