User: marongiu.luigi

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Posts by marongiu.luigi

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Comment: C: Failure in generating fastq from human fasta
... Hi, I tried FastqValidator but it only told me the obvious: $ fastQValidator --file ~/Downloads/sismi2Na_1.fq ERROR on Line 559644077: Incomplete Sequence. Finished processing /home/gigiux/Downloads/sismi2Na_1.fq with 559644077 lines containing 139911020 sequences. There were ...
written 5 weeks ago by marongiu.luigi380
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Comment: C: Failure in generating fastq from human fasta
... Thanks, I'll try that... ...
written 6 weeks ago by marongiu.luigi380
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Comment: C: Failure in generating fastq from human fasta
... that is exactly what i don't understand: how can the fastq be truncated? i followed the same strategy, that is converting a fasta into fastq, i did not touch the fastq, how did they get truncated? and how can i check what sequences are truncated? ...
written 6 weeks ago by marongiu.luigi380
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Failure in generating fastq from human fasta
... Hello, I have created some mutated human sequences modifying the GCRh38 fasta files. I then concatenated the files adn generated the fastq files with $ art -1 .../art/Illumina_profiles/custom/HiSeq2k_0m1.txt -2 ...art/Illumina_profiles/custom/HiSeq2k_0m2.txt -p -f 100 -l 140 -m 300 -s 10 -i hu ...
genome art next-gen fastqc written 6 weeks ago by marongiu.luigi380
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Comment: C: how to confirm that mapped read are accurate?
... good point! I'll try it... ...
written 6 weeks ago by marongiu.luigi380
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Comment: C: how to confirm that mapped read are accurate?
... Well, I wouldn't like that the reviewer comes with some 'below the waterline' question after all this work, so I' rather be sure of the data I gathered. The main problem is that I am aligning against a mix human-virus reference: I need to be sure that the reads are mapped against the virus genome an ...
written 6 weeks ago by marongiu.luigi380
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how to confirm that mapped read are accurate?
... Hello, I have aligned my reads against the reference genome using BWA, I removed the reads with low quality and deduplicated the alignment. How do I now that the results are correct? Do I need to prove that the reads are mapped correctly by using a second aligner (which should confirm the results ...
wgs next-gen confirmation quality control written 6 weeks ago by marongiu.luigi380
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Comment: C: Failure in confirming BWA mapping with BLASTN
... I tried but: $ blastn -task blastn -db nt -remote -query ~/Downloads/h32/confirm/query.fa BLASTN 2.9.0+ Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: ...
written 9 weeks ago by marongiu.luigi380
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Comment: C: Failure in confirming BWA mapping with BLASTN
... That is `right, fusion38-10k.fa` is built on the reference file i used for the BWA alignment, `blastDB/nt` is a local build of the human genome alone and then `-db nt -remote` is in remote. I'll try ` -task blastn-short` even if id did not used that option online... ...
written 9 weeks ago by marongiu.luigi380
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Failure in confirming BWA mapping with BLASTN
... Hello, I aligned my fastq files to a fusion genome made by the human GRCh38 and a virus genome that I called chrV. I extracted the starting position of the reads and the ending point, so that I can extract the sequence of interest with: samtools view -h -q 10 -f67 -F1408 $r_file $r_locus | grep -v ...
next-gen confirmation blastn sequencing written 9 weeks ago by marongiu.luigi380 • updated 9 weeks ago by JC8.8k

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