How to convert fastq to BAM

Question

[ja4123]

Hi! I would like to convert fastq file to bam i in oneliner: I have tried:

bowtie2 -x {input.index}/hg19.zip -U {input.fastq} | samtools view -b -o {output}

but it does not work. Anyone know how to do it? Kindly help.

[cmdcolin]

this is a useful link from the htslib docs https://www.htslib.org/workflow/fastq.html

if you wanted to use bowtie instead of minimap2, you can swap it out

Answer 1

[GenoMax]

See answer click -> : Piping bowtie2 output directly into BAM

[Jimpix]

I used: bowtie2 -x {input.index}/hg19.zip -U {input.fastq} | samtools view -bS -> {output}.bam from the site you have sent but I still have an error: Missing input files for rule fastq2bam: file.sam

[Pierre Lindenbaum]

but I still have an error: Missing input files for rule fastq2bam: file.sam

it's unrelated to your question. You have a problem with snakemake, not bowtie.

[Jimpix]

Thanks! I know where was a problem