User: Thibault D.

gravatar for Thibault D.
Thibault D.670
Reputation:
670
Status:
Trusted
Location:
European Union
Last seen:
32 minutes ago
Joined:
4 years, 10 months ago
Email:
t**************@outlook.fr

Posts by Thibault D.

<prev • 61 results • page 1 of 7 • next >
2
votes
1
answer
50
views
1
answers
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 1 day ago by Thibault D.670
1
vote
2
answers
319
views
2
answers
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 10 weeks ago by Thibault D.670
1
vote
2
answers
319
views
2
answers
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 10 weeks ago by Thibault D.670
1
vote
2
answers
319
views
2
answers
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 10 weeks ago by Thibault D.670
9
votes
2
answers
319
views
2
answers
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 10 weeks ago by Thibault D.670
1
vote
1
answer
406
views
1
answers
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 12 weeks ago by Thibault D.670
1
vote
1
answer
139
views
1
answers
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 3 months ago by Thibault D.670
1
vote
0
answers
369
views
0
answers
Comment: C: SARTools and batch effects
... Hi, as far as I read the doc, I think you can provide multiple columns and use a R-formula to give a more complex design to SARTools. Remember, it depends on the tool you're using within SARTools (DESeq2 or EdgeR). You may have to refer to their own documentations. ...
written 17 months ago by Thibault D.670
0
votes
1
answer
379
views
1
answers
Answer: A: STAR alignment command.
... Hi, It is not necessary, but the default value is 1 thread. In my experience, with human genomic data, increasing the number of threads above 10 is not very valuable. In any case, the number of threads just speeds up the process. It will **not** change your results, just the time you'll have to wa ...
written 17 months ago by Thibault D.670
3
votes
2
answers
1.1k
views
2
answers
Comment: C: building index with HISAT2
... I indeed made a mistake as I did not red the Hisat2 doc before answering. Hisat2 expects a comma-separated list of file, and my previous answer was a space-separated list of files. That is why the previous command produced many references. Parameters expansion with curly brackets produces a *space- ...
written 19 months ago by Thibault D.670

Latest awards to Thibault D.

Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For C: If I am in a right way in RNA-seq
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Cuffmerge or Cuffcompare?!
Popular Question 6 months ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 14 months ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 17 months ago, created a question with more than 1,000 views. For Understanding MMDiff output files
Popular Question 19 months ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: building index with HISAT2
Scholar 19 months ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Cuffmerge or Cuffcompare?!
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Bowtie2 vs Tophat Whats the difference
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Cuffmerge or Cuffcompare?!
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Why does TopHat return wrong XS-Strand attribute in BAM ?
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
Scholar 4.0 years ago, created an answer that has been accepted. For A: Bowtie2 reporting alignments count
Supporter 4.0 years ago, voted at least 25 times.
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Annotate transcript isoforms from Cufflinks GTF with splicing types
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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2265 users visited in the last hour