User: Thibault D.

gravatar for Thibault D.
Thibault D.690
Reputation:
690
Status:
Trusted
Location:
European Union
Last seen:
3 months, 1 week ago
Joined:
5 years, 7 months ago
Email:
t**************@outlook.fr

Posts by Thibault D.

<prev • 64 results • page 1 of 7 • next >
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Answer: A: No rule keywords allowed after run in snakefile
... Hi, Within the `run` section, you should use `snakemake.input["R1"]` instead of using wildcards. Or, use `snakemake.wildcards[...]`. If you do not mind, here are some unrelated advices: - Use the ["threads" keyword](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#threads) to hand ...
written 6 months ago by Thibault D.690
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Answer: A: STAR alignment EXITING because of FATAL ERROR: could not create output file
... Hi, STAR error is pretty clear to me: > Check if the path /home/c479e/ANTCoN_analysis/STAR/65312-RNA-FFPE_L001_ exists **and** you have permissions to write there Just run: `touch /home/c479e/ANTCoN_analysis/STAR/65312-RNA-FFPE_L001_` And if you get errors while *touch-ing*, try: `mkdir --par ...
written 8 months ago by Thibault D.690
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Comment: C: fGSEA result to csv
... Hi, have you tried to change your data type ? With functions like `base::as.data.frame()` ? ...
written 8 months ago by Thibault D.690
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Answer: A: If/else statement in Snakemake rule
... Hi, Within a `run` block, you have to write python compatible code. Here, the SyntaxError comes from Python itself and not Snakemake. Your `if` statements should end with a `:` at the end of the line: run: if params.alignment == "end2end": shell("bowtie2 -k 1 -p 6 -x hg19 ...
written 9 months ago by Thibault D.690
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Comment: C: If I am in a right way in RNA-seq
... > % of reads unmapped: too short | 99.42% You know where the problem is. I'll let you search what is your expected read size in STAR (index creation), then compare it to your actual read size (in your fastq file, or with FastQC). ...
written 11 months ago by Thibault D.690
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Comment: C: If I am in a right way in RNA-seq
... Look at the logging files and do not hesitate to run quality metrics tests with either `samtools flagstats`, or `picard CollectAlignmentSummaryMetrics`. Neither runtime, nor file size are reliable indicators of a "good" result. ...
written 11 months ago by Thibault D.690
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Comment: C: If I am in a right way in RNA-seq
... This error does not come from STAR, but from your scheduler (Torque). Probably reservation issues, however I do not have enough information with your post. ...
written 11 months ago by Thibault D.690
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Answer: C: If I am in a right way in RNA-seq
... Hi, Your work looks fine to me, however, let me point some improvements: STAR can give you coordinate-sorted bam-compressed alignement file, which makes your picard + samtools not necessary. Look at the option `--outSAMtype BAM SortedByCoordinate`. You're working on cancer data, which will contai ...
written 11 months ago by Thibault D.690
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Answer: A: Snakemake input and wildcards
... Hi, The error points out your problem: you have only one rule. This rule is therefore your 'target rule'. A target rule shall not contain any wildcard. Basically, when you have wildcards in the input section, you should also find them in the output one. See examples at the [front page](https://sna ...
written 11 months ago by Thibault D.690
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Answer: A: When (not to) pre-build a STAR index
... AFAIK, unless it is clearly written by developers, I build one index for a genome version/patch, for one version of a software (either majors or minors). There is not software I know deep enough to be 100% sure the last commit did not change the index, even by a single *maybe-very-important* octet. ...
written 12 months ago by Thibault D.690

Latest awards to Thibault D.

Scholar 6 months ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Popular Question 7 months ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Appreciated 11 months ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For C: If I am in a right way in RNA-seq
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Cuffmerge or Cuffcompare?!
Popular Question 15 months ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 23 months ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: building index with HISAT2
Scholar 2.3 years ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Cuffmerge or Cuffcompare?!
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Bowtie2 vs Tophat Whats the difference
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Appreciated 4.2 years ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Popular Question 4.3 years ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Scholar 4.7 years ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Supporter 4.8 years ago, voted at least 25 times.
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types

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