User: marongiu.luigi

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510
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Germany, Mannheim, UMM
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Posts by marongiu.luigi

<prev • 443 results • page 1 of 45 • next >
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Comment: C: How to test transposition in BAM files?
... These seem promising, I'll read them, thank you. ...
written 5 days ago by marongiu.luigi510
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How to test transposition in BAM files?
... Hello, is there a good pipeline for the analysis of transposition using WGS data? In other words, that is the procedure to assess whether a transposon has jumped between one sample and another? Thank you ...
assembly trasnposition sequencing written 6 days ago by marongiu.luigi510
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Comment: C: sambamba-sort: Error reading BGZF with BAM file
... Thanks, I overlooked the conversion -- that's why the file was so large. Usually, I pipe everything including samtool sort. Is there a better tool to sort a large bam file? ...
written 9 days ago by marongiu.luigi510
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sambamba-sort: Error reading BGZF with BAM file
... I have aligned a file with BWA MEM but since the file is big (1 Tb) I could not sort it with samtools due to memory limits. I tried with sambamba but I got an error: $ bwa mem -t 12 > .bam $ sambamba sort -o _AlnSrt.bam .bam sambamba-sort: Error reading BGZF block starting from ...
software error sort sambamba written 9 days ago by marongiu.luigi510 • updated 9 days ago by ATpoint35k
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What species are indicators of environmental contamination in metagenomic studies?
... Hello, I am carrying out a metagenomic study and I would like to know if there are studies listing microbial species associated with environmental contamination. If I find, for instance, crAssphage in stools, this virus is reported as a common presence in the intestinal locus. Is this virus present ...
wgs alignment contamination rna-seq assembly written 6 weeks ago by marongiu.luigi510 • updated 6 weeks ago by colindaven2.2k
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Comment: C: Is there a model for detection of few reads for low abundance targets?
... Er -- no... The decoy is there but I did not include it in the analysis. Perhaps I should have a look at it, thanks for the tip. Anyway, this happens for all other viruses, not only the herpes ones... ...
written 6 weeks ago by marongiu.luigi510
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Comment: C: Is there a model for detection of few reads for low abundance targets?
... Sorry: the experiment is a simple WGS of human samples; I am looking at the leftover do not aligned to human chromosomes; the coverage is 25x; sequences are filtered as phred 33 plus blastn and blastx to remove false positive detection of viral sequences. The endogenous retrovirus I am showing is HE ...
written 6 weeks ago by marongiu.luigi510
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Is there a model for detection of few reads for low abundance targets?
... Hello, Is there a model (or a reason) why genome with low abundance only show a few portions of the reference genome? I am doing a WGS on virus sequences; the mean coverage was 25, and for endogenous retroviruses I have such kind of coverage: ![enter image description here][1] But for other, suc ...
wgs next-gen alignment sequencing written 6 weeks ago by marongiu.luigi510
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use samtools stats to plot quality of alignment
... Hello, I got an alignment-to-human obtained via BWA and I deduplicated the bam file. I would like to visualize the quality of the alignment with R in order to have complete control on the graphic. I used `samtools stats` to get the basic information but how is the output formatted? I can see that ...
alignment visualization quality control written 8 weeks ago by marongiu.luigi510 • updated 8 weeks ago by ATpoint35k
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Comment: C: Interpretation of sparse reads
... Hello, this is a WGS; I align against a human+virus. I actually selected reads with 30 MQ, but left 10 on IGV to have a more thorough look. I will read your pipeline, thank you. ...
written 9 weeks ago by marongiu.luigi510

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