User: kaz0816

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kaz08160
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Posts by kaz0816

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Comment: C: Extract reads based on the orientation of the mapped reads.
... I understand that the "bamtools split" command retrieves those reads. However, I still don't know the FLAG setting when dividing into pair-end reads (LR:-> <-), mate pair (RL: <- ->) and others (RR or LL). I would appreciate it if you could explain it in an easy-to-understand manner. ...
written 10 weeks ago by kaz08160
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Extract reads based on the orientation of the mapped reads.
... I want to extract reads from a BAM file based on the orientation of the mapped reads. I want to extract the reads of each category separately based on the orientation of the reads such as LR (Illumina pair-end reads), RL (Illumina mate-pair reads), RR or LL as depicted in IGV. Please tell me if ther ...
genome mate-pair dna-seq paired-reads mapping written 10 weeks ago by kaz08160 • updated 10 weeks ago by colindaven2.5k
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Comment: C: How to remove bases out of codon frame
... Raw data are nucleotide sequences and amino acid sequences from 4 species in FASTA format. Nucleotide sequences do not necessarily start with an open reading frame, but with one or two extra bases. On the other hand, the amino acid sequences does not start with a "X" to correspond to the extra bases ...
written 5 months ago by kaz08160
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How to remove bases out of codon frame
... Please tell me how to efficiently remove bases that are out of the codon frame as follows. Protein: [N-ter]- S D C V E I L T N C A -[C-ter] Nucleotide: [5']- G TCA GAC TGC GTA GAA ATT CTT ACA AAT TGT GCA GA -[3'] I aligned the nucleotide sequences based on the amino aci ...
alignment sequence written 5 months ago by kaz08160
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Extract single transcript sequences from genome assembly
... Hi, I want to extract one transcript per gene from the genome assembly and its GFF3 file registered in Refseq. And I want to extract a transcript that has a longest or a certain frame. Anyone know of an efficient method? I am looking for this method to do ortholog comparisons. Best regards, ...
genome assembly written 5 months ago by kaz08160

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