User: giovannaventola3es9

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Posts by giovannaventola3es9

<prev • 19 results • page 1 of 2 • next >
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Comment: C: RNASeq with mixed tissues
... bbsplit.sh in1=reads1.fq in2=reads2.fq ref=human.fa,mouse.fa ambiguous2=toss basename=out_%.fq refstats=Statistics_%.txt then I used directly STAR: STAR --runMode alignReads --runThreadN 12 --genomeDir Genomes/STARversion2.70f/STARversion2.70f_INDEX_HG38_GenCode_v29/ --sjdbGTFfile Genomes ...
written 6 days ago by giovannaventola3es920 • updated 6 days ago by genomax67k
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Comment: C: BBSplit xenograft Human-Mouse- RawCount
... RefStats of one of my samples: name %unambiguousReads unambiguousMB %ambiguousReads ambiguousMB unambiguousReads ambiguousReads assignedReads assignedBases HG38 90.69745 4525.569508 6.03784 301.545669 59646218 3970720 63616938 4827115177 mm10 2.89875 144.634382 6.03784 301.545669 190633 ...
written 6 days ago by giovannaventola3es920 • updated 6 days ago by genomax67k
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Comment: C: RNASeq with mixed tissues
... When I use featureCount I get reads % that map to exons that are too low, while STAR percentages are greater than 80%, Assuming the same annotation file. WHY? ...
written 6 days ago by giovannaventola3es920
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BBSplit xenograft Human-Mouse- RawCount
... Hi, I have a problem with BBsplit. I have xenograft mouse-human rna-seq samples (paired fastq) and I had thought to using BBSplit to delete the mouse contamination. So I used this command line: bbsplit.sh in1=reads1.fq in2=reads2.fq ref=human.fa,mouse.fa ambiguous2=toss basename=out_%.fq ref ...
rna-seq written 7 days ago by giovannaventola3es920 • updated 7 days ago by genomax67k
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Comment: A: Tool to separate human and mouse rna seq reads
... sorry, I have a problem with BBsplit. I have xenograft mouse-human rna-seq samples and I had thought to using BBSplit to delete the mouse contamination. So I used this command line: bbsplit.sh in1=reads1.fq in2=reads2.fq ref=human.fa,mouse.fa ambiguous2=toss basename=out_%.fq refstats=Statistics_%. ...
written 7 days ago by giovannaventola3es920
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Comment: C: BBSplit syntax for generating builds for the reference genome and how to call di
... yes, but after I use BBsplit, I obtain the fastq file and then I can to remap this with STAR but the count? FeatureCount doesn't work well with bbsplit. So my question is: After BBsplit What can I use to map and to calculate the count? Thanks ...
written 7 days ago by giovannaventola3es920
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Comment: C: Truncated bamtofastq output files.
... yes, but after I use BBsplit, I obtain the fastq file and then I can to remap this with STAR but the count? FeatureCount doesn't work well with bbsplit. So my question is: After BBsplit What can I use to map and to calculate the count? Thanks ...
written 7 days ago by giovannaventola3es920
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Comment: C: RNASeq with mixed tissues
... yes, but after I use BBsplit, I obtain the fastq file and then I can to remap this with STAR but the count? FeatureCount doesn't work well with bbsplit. So my question is: After BBsplit What can I use to map and to calculate the count? Thanks ...
written 7 days ago by giovannaventola3es920
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Comment: C: Circular Genome??
... Sorry, but can you tell me how to do this? Thaks a lot ...
written 5 months ago by giovannaventola3es920
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Comment: C: How can Investigate if a Viral genome is circular or linear? And if it is single
... I had paired fastq file that were mapped with Genieous and I obtained the contigs fasta file. Then I performed SOPRA scaffolding and the statistics of its. Now I would like to know if my genome is single or double stranded and if it is circular or linear. Now I'm testing Circlator, but it is still r ...
written 5 months ago by giovannaventola3es920

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