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User: Corentin

gravatar for Corentin
Corentin • 150
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Posts by Corentin

<prev • 23 results • page 1 of 3 • next >
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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 14 days ago by Corentin • 150
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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 14 days ago by Corentin • 150
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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 14 days ago by Corentin • 150
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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 weeks ago by Corentin • 150
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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 weeks ago by Corentin • 150
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... Yes, you're right (I was, wrongly, thinking about STAR, which produces by default a sam which contains only the aligned read) ...
written 4 weeks ago by Corentin • 150
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Comment: C: bwa-mem, from .sam/.bam to fasta file
... The size of the bam depends on how many reads mapped to the reference. Also, be aware that bwa mem outputs a SAM file by default, not a BAM. ...
written 4 weeks ago by Corentin • 150
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Comment: C: Remove sequences without alignment in mummerplot
... I tried but the sequences still appear in the dot plot, like before as an empty line. ...
written 4 weeks ago by Corentin • 150
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Remove sequences without alignment in mummerplot
... Hi, I aligned a scaffold assembly to a closely related species with Mummer. So, this is a "many vs one" approach. I am happy with the tool. However, when I produce the dot plot on the filtered alignments (I used delta-filter using the "-1" option to get unique alignments) the plot contains scaffo ...
mummer mummerplot written 4 weeks ago by Corentin • 150
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Comment: C: Platanus only use single thread
... Yes, that what I expected. But I was just thinking that the de Bruijn graph construction would be parallelized, maybe it is not implemented yet. ...
written 3 months ago by Corentin • 150

Latest awards to Corentin

Appreciated 9 months ago, created a post with more than 5 votes. For A: Selecting fastq sequences
Scholar 9 months ago, created an answer that has been accepted. For A: expression to networking
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: expression to networking
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
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