Hi! I would like to ask what is the difference between commands bellow. This wrote in oneliner:
bowtie2 -x {input.index} -U {input.fastq} | samtools view -bS -> {output}
and this two:
bowtie2 -x {input.index} -U {input.fastq} -S {output}
samtools view -u {input} -o {output}
or this is the same or the first one is shorter?
1 answer
Using the first option, the output will be directly a BAM file.
Using the second option, you will get a SAM file from the first command, and a BAM file from the second. If you don't need a SAM file, I will recommend going for the first option, it is faster and you will avoid generating huge SAM files in your computer that take a lot of space and you don't need them.
Hi! No problem. I have never used -u myself. Here you can read the manual of samtools, which says the same as what @GenoMax has pointed out, and also This option saves time spent on compression/decompression and is thus preferred when the output is piped to another samtools command. I guess the output is a SAM file instead of a BAM file, or some kind of uncompressed file, and that is why is bigger. You can try to see the content of the file. A BAM file is always compressed.
Log in to answer this question.
-
how to effectively pipe chromap into samtools view
written by Matteo Ungaro •
-
samtools idxstats not removing ChrM
written by Jen •
-
How to convert fastq to BAM
written by ja4123 •
-
How to generated unaligned .sam file using bowtie2
written by wangxiong •
-
Alignment fastq files
written by Jimpix •
-
Bowtie2 unpaired mode usage
written by Jimpix •
-
Piping bowtie2 output directly into BAM
written by hersh •
-
Naive BASH question on top to bottom programming regarding my alignment script
written by datascientist28
-
Are the BAM files from tophat and bowtie-samtools the same?
written by jolin0701-dy
-
error of samtools sort
written by jolin0701-dy
