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Posts by rohita.sinha
... 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 ...
... Thanks for the answer. As I had opted to put "-a", I think bowtie2 should allow reads to map to all possible positions. ...
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 ...
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