User: Corentin

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Corentin170
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Posts by Corentin

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Comment: C: Good mean coverage but big std in coverage
... "Good enough" is subjective and depends on your experiment, your genome, your reads quality etc... But the higher the percentage of mapped read the better. You can look in the literature and tutorials for additional steps to check and analyse your data. RNA-seq is a popular method and a lot of reso ...
written 9 weeks ago by Corentin170
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Answer: A: Good mean coverage but big std in coverage
... Hello, From this report only it would seems that almost all your reads mapped to a very small portion of your genome. Do not forget that rna-seq will only map to protein-coding parts of your genome which is estimated (in humans) as 2% of the genome total size. Moreover, in rna-seq the coverage depe ...
written 9 weeks ago by Corentin170
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Answer: A: Plot gene counts of different groups in the same graph
... If you do not care about individual genes you can create a boxplot, one for each group. It will tell you how the overall expression is different. If you care about individual genes and you do not have a lot of them, you can create a bar plot for each. For example, you can use **geom_bar** with the ...
written 11 weeks ago by Corentin170
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Answer: A: Assessing The Quality Of De Novo Assembled Data
... This is an old topic but here is a list of the tool I currently use: - Quast, probably the most used tool to get assembly statistics, such as N50, #contigs, size of the largest contig etc... http://quast.bioinf.spbau.ru/manual.html - Busco, this is a set of manually curated othologous genes, usefu ...
written 12 weeks ago by Corentin170
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Comment: C: Can renaming, copying, or moving the omics data file corrupt it?
... Try to launch "samtools quickcheck" on your sam / bam file. It should give you more information about the issue. ...
written 12 weeks ago by Corentin170
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Comment: C: Get the regions mapped by the same reads
... I think I will use these commands to get the multiple mapped reads and then get the other regions from the XA flag, thanks ! ...
written 3 months ago by Corentin170
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Comment: C: Get the regions mapped by the same reads
... No, I only have one bam file, and I am looking for reads that map to multiple regions in this one bam. ...
written 3 months ago by Corentin170
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Get the regions mapped by the same reads
... Dear all, I have a bam file and a bed file (with a thousand regions). I would like, for each region in the bed, to get all the reads that mapped to this region (relatively straightforward) but I also want to get, if any, other regions mapped by these same reads. I could not find something useful ...
reads bed bam multiple alignments sam written 3 months ago by Corentin170
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... Also, if you wish to visualise the content of a BAM file you can use "samtools view *out.bam*" ...
written 4 months ago by Corentin170
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... With STAR you can use the "--outReadsUnmapped" option to get the unmapped reads in a separate bam. I guess that you can get the original fastq by using both the "Aligned.out.sam" and the "unmapped.bam" ...
written 4 months ago by Corentin170

Latest awards to Corentin

Appreciated 12 months ago, created a post with more than 5 votes. For A: Selecting fastq sequences
Scholar 12 months ago, created an answer that has been accepted. For A: expression to networking
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: expression to networking
Scholar 15 months ago, created an answer that has been accepted. For A: expression to networking
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: expression to networking

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