User: marongiu.luigi

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Germany, Mannheim, UMM
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Posts by marongiu.luigi

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Answer: A: how to download all reference files with ensembl and taxon ID?
... I have found it: esearch -db "nucleotide" -query "txid10239 [Organism] AND refseq[filter]" | efetch -format fasta > ref.fa Case closed. ...
written 18 days ago by marongiu.luigi520
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how to download all reference files with ensembl and taxon ID?
... Hello, I would like to download all the reference sequences of viruses deposited. I remember this could be done with esearch/efetch and the taxon ID of the species of interest (I believe viruses have ID 10239). I am trying with: esearch -db taxonomy -query 10239 | efetch -format=fasta > re ...
ensembl efetch sequence esearch written 18 days ago by marongiu.luigi520
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Comment: C: What is the story behind chrEBV?
... In this case, it is true. There was much more on Google than PubMed... ...
written 11 weeks ago by marongiu.luigi520
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What is the story behind chrEBV?
... Hello, is there some reference to the EBV decoy (I think that is the official name) aka `chrEBV` present in the human assembly GChr38 (and previous)? why and where was it introduced? by whom? On PubMed I got > your search for chrEBV retrieved no results Same thing for EBV decoy. Thank you ...
genome assembly next-gen written 11 weeks ago by marongiu.luigi520
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Comment: C: Can I get a hit by WGS but not by PCR?
... On IGV the positive (bottom alignment) looks like this: ![enter image description here][1] This sample had 10 reads about 100 bp each. By extracting the EBV chromosome, I got these for the positive WGS / negative PCR sample: samtools view -b -h "chrEBV" | samtools flagstat 95 + 0 in tota ...
written 12 weeks ago by marongiu.luigi520
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Comment: C: Can I get a hit by WGS but not by PCR?
... I am not concerned about the one negative PCR but the two positive ones: they disprove the WGS analysis... I used a concatenated genome with all the viral sequences in GeneBank, added it to the human genome and aligned with BWA. But simple there are no reads. ...
written 12 weeks ago by marongiu.luigi520
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Can I get a hit by WGS but not by PCR?
... Hello, I performed a WGS with Illumina on three histological sections. I looked for viral genomes and I got one hit for Epstein-Barr virus. Then I performed PCR to confirm the data and I got an unclear result for the sample positive by WGS and two positives for the other two samples. How shall I c ...
sequencing next-gen confirmation pcr written 12 weeks ago by marongiu.luigi520 • updated 8 weeks ago by Biostar ♦♦ 20
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Comment: C: How to test transposition in BAM files?
... These seem promising, I'll read them, thank you. ...
written 3 months ago by marongiu.luigi520
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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 3 months ago by marongiu.luigi520
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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 3 months ago by marongiu.luigi520

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