Hello everyone!
I'm new analyzing transcriptomic.
I have small RNA-seq data, single-end from Rat.
Initially, I mapped the data with Bowtie with next command:
bowtie -p 50 --mm -n 0 --best --strata -m 1 /media/stdata/bowtie1_index/rn6/rn6_bw1 -q $each_file\.fastq -S $each_file\_n0_m1.sam
** -n 0 and -m 1, because we are probing parameters.
After, I noticed that the kit to make library was "TruSeq® Small RNA Library".
Reading in the web, I found that:
"For example, the Illumina TruSeq small RNA sample preparation kit produces strand-specific libraries. The kit specifically selects the RNA species that have a monophosphate group at its 5′-end and a hydroxyl group at 3′-end, a typical structure for miRNAs."
LINK: https://www.liebertpub.com/doi/full/.../nat.2012.0367
Then, I think that bowtie also must have option for strand-specific.
Considering that the data is single-end and default is --fr, Must I need to add option for strand-specific?
If so, what options are they?
I found:
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)
--nofw/--norc do not align to forward/reverse-complement reference strand
But I have single end, so I think is necessary to use "--nofw/--norc", but I'm confused which one to choose.
I'm new analyzing transcriptomic.
I have small RNA-seq data, single-end from Rat.
Initially, I mapped the data with Bowtie with next command:
bowtie -p 50 --mm -n 0 --best --strata -m 1 /media/stdata/bowtie1_index/rn6/rn6_bw1 -q $each_file\.fastq -S $each_file\_n0_m1.sam
** -n 0 and -m 1, because we are probing parameters.
After, I noticed that the kit to make library was "TruSeq® Small RNA Library".
Reading in the web, I found that:
"For example, the Illumina TruSeq small RNA sample preparation kit produces strand-specific libraries. The kit specifically selects the RNA species that have a monophosphate group at its 5′-end and a hydroxyl group at 3′-end, a typical structure for miRNAs."
LINK: https://www.liebertpub.com/doi/full/.../nat.2012.0367
Then, I think that bowtie also must have option for strand-specific.
Considering that the data is single-end and default is --fr, Must I need to add option for strand-specific?
If so, what options are they?
I found:
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (default: --fr)
--nofw/--norc do not align to forward/reverse-complement reference strand
But I have single end, so I think is necessary to use "--nofw/--norc", but I'm confused which one to choose.
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