Moderator: Ido Tamir

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Ido Tamir4.7k
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Austria
Last seen:
3 days ago
Joined:
6 years, 2 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 • 283 results • page 1 of 29 • next >
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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 22 days ago by Ido Tamir4.7k
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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 6 weeks ago by Ido Tamir4.7k
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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 7 weeks ago by Ido Tamir4.7k
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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 7 weeks ago by Ido Tamir4.7k
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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 3 months ago by Ido Tamir4.7k
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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 3 months ago by Ido Tamir4.7k
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Answer: A: R multiple parameters
... better ask on generic R questions on stackoverflow or the R mailing list and include a simply reproducible input. I would switch to ggplot2 where you plot from a "long" data frame - each observation in its own row. library("reshape2") library("ggplot2") library("phyloseq") data(Gl ...
written 5 months ago by Ido Tamir4.7k
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Answer: A: How to run Galaxy pipeline using a python code (is there a module, package for g
... Look at bioblend: http://bioblend.readthedocs.io/en/latest/api_docs/galaxy/docs.html it wraps galaxys REST API Ask more questions at: https://biostar.usegalaxy.org/ ...
written 7 months ago by Ido Tamir4.7k
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Comment: C: Deciding for the threshold for scores?
... Hehe! how often did you hope for this and it turned out like this? ...
written 11 months ago by Ido Tamir4.7k
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Comment: C: How to imagine the future of bioinformatics?
... yes and the mars mission also brought back a new viral strain that kills the population that fled inland because of the rising sea levels ... ...
written 11 months ago by Ido Tamir4.7k

Latest awards to Ido Tamir

Scholar 5 weeks ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Scholar 5 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 9 months ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Appreciated 11 months ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Popular Question 15 months ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Picking A Programming Language And Where To Begin
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Appreciated 23 months ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Popular Question 23 months ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Pundit 2.1 years ago, created a comment with more than 10 votes. For C: Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinf
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Picking A Programming Language And Where To Begin
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Picking A Programming Language And Where To Begin
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
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Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: Tophat Library Type And Pair Orientation For Illumina Data
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: Fastq Format Confusion
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Appreciated 3.0 years ago, created a post with more than 5 votes. For C: Converting Python Code To R

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