Moderator: Ido Tamir

gravatar for Ido Tamir
Ido Tamir5.1k
Reputation:
5,140
Status:
Trusted
Location:
Austria
Last seen:
1 day, 14 hours ago
Joined:
9 years, 6 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 • 328 results • page 1 of 33 • next >
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Comment: C: How to fill with dots empty fields in a dataframe in R when splitting a column b
... please mark the best answer as accepted, upvote other useful answers and write any thanks into comments and not as an answer ...
written 11 weeks ago by Ido Tamir5.1k
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Comment: C: Data management in R, perl or python
... they want the suffix after the 2 letters collected and appended. This is a basic programming question for which they should show at least some effort in some language ...
written 3 months ago by Ido Tamir5.1k
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Answer: A: New data transformation tool for Windows and Mac
... This looks a lot like simplified knime https://www.knime.com/ which has an open source gui besides commercial offerings ...
written 4 months ago by Ido Tamir5.1k
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Comment: C: how to get total read count, mapped read count and unmapped read count from mult
... you are asking two questions: a) how to loop over files b) how to extract mapped counts. a) is not really a topic for this site and you can find answers on stackoverflow or google. b) was answered multiple times. ...
written 4 months ago by Ido Tamir5.1k
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Comment: C: RNA-Seq and no of reads
... https://hbctraining.github.io/Intro-to-rnaseq-hpc-O2/lessons/03_alignment.html ...
written 4 months ago by Ido Tamir5.1k
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Comment: C: Running a code in batch mode on a list of files
... you seem to be wrinting everything into out. im not good with bashs quoting rules, so to be safe: for i in $(find ..); do awk 'cmd' $f > ${f}_out.txt ; done This is a rather complicated statement and you should create a script from it that you can (re)use in a loop and reuse it. Saves time i ...
written 5 months ago by Ido Tamir5.1k
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Comment: C: Extracting rows on basis of specific column values in R
... please work through any of the many online R tutorials. You could also look up "how to ask questions" and unfortunately it looks like a correct tagging of posts tutorial is also necessary. Maybe you think the $ would signify a regex end matching? try endsWith ...
written 5 months ago by Ido Tamir5.1k
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Comment: C: Trouble with choosing the right reference transcriptome file for mm10
... the ncrna in the name could already give you a hint what the file represents - so I would change the file you use. But this is completely independent of the question why you think that two different programs should deliver identical results for a complex task implemented with different assumptions ...
written 5 months ago by Ido Tamir5.1k
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Answer: A: RNA-Seq differential gene expression without biological and technical replicates
... https://www.biostars.org/p/398152/ maybe look at NOI-Seq http://seqanswers.com/forums/showpost.php?p=107433&postcount=2 or just do it in excel: sort by ratio from high to low, same reliability (but no normalisation). The result is not to be trusted. It would have been better to use just 1 deve ...
written 6 months ago by Ido Tamir5.1k
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Answer: C: How to get DE genes without replicates using EdgeR
... in the 2. part you called differential expression on a matrix without gene names as row names filled with random numbers ...
written 6 months ago by Ido Tamir5.1k

Latest awards to Ido Tamir

Popular Question 16 days ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Scholar 7 weeks ago, created an answer that has been accepted. For A: R multiple parameters
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Scholar 22 months ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: Picking A Programming Language And Where To Begin
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Scholar 3.5 years ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Scholar 3.8 years ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Good Answer 4.2 years ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Appreciated 4.3 years ago, created a post with more than 5 votes. For A: Shall We Go Back To Stackexchange?
Good Answer 4.3 years ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Popular Question 4.6 years ago, created a question with more than 1,000 views. For Duplication And Quality Control In Published Ngs Data
Commentator 4.6 years ago, created a comment with at least 3 up-votes. For C: Picking A Programming Language And Where To Begin
Good Answer 4.8 years ago, created an answer that was upvoted at least 5 times. For A: Illumina Read Names: /2 Vs. /3
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Shall We Go Back To Stackexchange?

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