User: caggtaagtat

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caggtaagtat860
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Posts by caggtaagtat

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Comment: C: snakemake: pipeline failed with MissingOutputException
... Ok, than I think an alternative solution could be to submit the jobs similar to this, depending on the "job scheduler" on your cluster ...
written 4 days ago by caggtaagtat860
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Comment: C: snakemake: pipeline failed with MissingOutputException
... I see. You can simualte a "clsuter" on your mashien, thats why I got confused about. You are right, the OP want to execute it on a regular cluster, so my answer is still relevant. Coming back to your question above: When you had 100 samples this snakemake script would try to submit 100 job to the c ...
written 4 days ago by caggtaagtat860
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Comment: C: snakemake: pipeline failed when submit to cluster
... Please excuse me, I was under the impression, that you wanted to submit the jobs to an High-Performing-Cluster. I just re-read your question and saw that you want to execute it on your local mashine. ...
written 5 days ago by caggtaagtat860
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Answer: A: snakemake: pipeline failed when submit to cluster
... Hi there, since you want to submit jobs to the cluster, I would like to share a nice way to do so. You can write the STAR command in a shell script, lets call it `STAR.sh` and then submit it to the cluster like this: rule align_with_STAR_pass1: input: "{samples}.fq" ...
written 5 days ago by caggtaagtat860
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Comment: C: Running STAR with --twopassMode Basic
... Hi lucas.caue.jacintho, I'm glad it helped :) ...
written 6 days ago by caggtaagtat860
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Answer: A: Running STAR with --twopassMode Basic
... Hi there, you can do two-pass-mapping manually by splitting up the process. I read about it in some google group with developer Alex: So this is an example for single end data with an average length of 150nt. ###First you do the first STAR alignment: #Enter the right directory cd /path_ ...
written 8 days ago by caggtaagtat860
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Comment: C: STAR mapping results
... This high amount of "too short" reads could also be the result, when you have paired end reads which are not sorted correctly. ...
written 8 days ago by caggtaagtat860
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Comment: C: RNAseq differential expression analysis : no significative FDR but significative
... Hi, Be aware, that during DGE analysis you are looking at differences on the gene level. When for instance, the severity of the cancer developement comes from an higher amount of erroneously spliced mRNA transcripts in one sample group, the summarized gene expression stays the same, because every r ...
written 20 days ago by caggtaagtat860
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Comment: C: STAR mapping results
... I never worked with Hisat2, but I would guess they should be around the same. Out of curiosity, did you check for rRNA content in the samples with for example the tool sortMeRNA? Analysing relatively old data, I came across rRNA contents of around 20-40% of total reads after mRNA enrichment. So that ...
written 7 weeks ago by caggtaagtat860
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Answer: A: Making genome-wide transcription level track from transcript level count
... Hi, I don't know about how to convert the data from salmon. I read, that you can generate pseudobam files with kalisto and maybe there is an tool for the output of salmon. Concerning the STAR coverages, you get more reads, because it also counts gapped reads, which are not part of an already annot ...
written 7 weeks ago by caggtaagtat860

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Popular Question 3 days ago, created a question with more than 1,000 views. For What does the transcript support level (TSL) from ensembl mean?
Scholar 6 days ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Scholar 7 weeks ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: How to create custom gtf annotation file?
Popular Question 3 months ago, created a question with more than 1,000 views. For What does the transcript support level (TSL) from ensembl mean?
Appreciated 4 months ago, created a post with more than 5 votes. For A: Question about exon/intron counting in RNA-seq dataset analysis
Popular Question 5 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Appreciated 6 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?
Scholar 6 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 6 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Scholar 7 months ago, created an answer that has been accepted. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Popular Question 8 months ago, created a question with more than 1,000 views. For Trimming single end reads for STAR?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Ovation RNA-seq system, bionfomatic alignment and htseq-count
Scholar 8 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Popular Question 11 months ago, created a question with more than 1,000 views. For STAR do i need --twopassMode ?
Scholar 13 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: what do the headers of the rMATS output files mean?
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Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: what do the headers of the rMATS output files mean?
Scholar 18 months ago, created an answer that has been accepted. For A: Only 1% of reads are used as "input reads" in STAR
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Appreciated 20 months ago, created a post with more than 5 votes. For A: what do the headers of the rMATS output files mean?

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