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Alignment fastq files

I have a question. I need to align and convert fastq files (unpaired) into bam file. If to beo sure I need to ast first if this command below are enough to do this or I forgot about something.

bowtie2 -x input.index.hg19 -U input.fastq -S {output}

and then:

samtools view -u input.sam -o output.bam

If it is something that I forgot, (what I need to take int consideration) I ask because my further pipeline does not work like it should.

Kindly help.

samtools bowtie2 alignment
• 2,156 views • link
updated by Ram Ram • written by Jimpix • Jimpix

1 answer

You should include all of your code leading up to this point and the error you are getting in your pipeline, otherwise we can't really give any specific advice.

As a side note, if all you want is the BAM file, you can pipe the output of bowtie2 to samtools directly.

bowtie2 -x input.index.hg19 -U input.fastq | samtools view -b - -o output.bam
• 0 views • link
written by rpolicastro rpolicastro

Thanks for advice by my pipeline is quite long and working like it is, just the result are not expected. But that what you have wrote is exactly the same just short?

• 0 views • link
written by Jimpix • Jimpix

I saw on the Bowtie2 website indexes like:

  • H. sapiens, hg19 UCSC
  • H. sapiens, hg19 + major SNVs UCSC+1KG (How we built this, FASTA)
  • H. sapiens, hg19 + major SNVs & indels, UCSC+1KG, (How we built this, Use with levioSAM, FASTA)

I need just hg19 bowtie index, can someone tell me which they differ? And which should I chosse?

• 0 views • link
written by Jimpix • Jimpix

the first one will be fine, the others have some variant information from the 1000Genomes project incorporated. I'd just take the first one if you really need hg19, or better use hg38 which is the current reference genome.

• 0 views • link
written by ATpoint ATpoint

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