User: rohita.sinha
rohita.sinha • 0
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Posts by rohita.sinha
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... 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 ...
written 7.8 years ago by
rohita.sinha • 0
• updated
17 months ago by
Biostar ♦♦ 20
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... Thanks for the answer. As I had opted to put "-a", I think bowtie2 should allow reads to map to all possible positions.
...
written 7.8 years ago by
rohita.sinha • 0
1
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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 ...
written 7.8 years ago by
rohita.sinha • 0
• updated
4.8 years ago by
Biostar ♦♦ 20
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