Alignment fastq files

Question

[Jimpix]

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.

Answer 1

[rpolicastro]

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

[Jimpix]

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?

[ATpoint]

Yes

[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?

[ATpoint]

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.