User: rohita.sinha

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Posts by rohita.sinha

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Illumina Pe Reads Mapping To Reference Genome
... I have around 300 metagenomic sample set of PE-illumina reads. Assembly of these reads give me fairly longer contigs and I can map around 80-90% of my reads back to these contigs. But when I map same reads to ~5000 complete microbial reference genomes, only a small fraction of reads (2%-8%) are m ...
illumina metagenomics reference bowtie2 written 6.8 years ago by rohita.sinha0 • updated 5 months ago by Biostar ♦♦ 20
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Answer: A: Bowtie2 Mapping Different Number Of Reads To Same Sequence When Ref-Seq Is Part
... Thanks for the answer. As I had opted to put "-a", I think bowtie2 should allow reads to map to all possible positions. ...
written 6.8 years ago by rohita.sinha0
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Bowtie2 Mapping Different Number Of Reads To Same Sequence When Ref-Seq Is Part Of Different Indexes
... I am using bowtie2 to map my PE reads. I have indexed multiple bacterial genomes by putting them together in a multi-fasta file fashion. bowtie2 -q -a -p 1 -x Multi -1 R100_1.fq -2 R100_2.fq -U 100_Orph.fastq -S 100.sam samtools view -b -S 100.sam -o 100.bam coverageBed -abam 100.bam -b BED_RefSe ...
bedtools bowtie2 written 6.8 years ago by rohita.sinha0 • updated 3.9 years ago by Biostar ♦♦ 20

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