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hi everyone,
i have clipped my raw reads to get rid of poor quality reads by using The Nesoni clip: tool(http://thegenomefactory.blogspot.com...eads-with.html)
and i got clipped_R1.fq , clipped_R2.fq and clipped_single.fq(orphan reads) files . now i wanna align all these reads to reference sequences and then get FPKM value. so i used bowtie2 :
(http://bowtie-bio.sourceforge.net/bo...al.shtml#usage)
i wrote this:
but that did not work.
can i do that alignment that paired end and orphan reads at the same time to reference sequences
? if i could, how 
? could anyone give me some suggestions?
i have clipped my raw reads to get rid of poor quality reads by using The Nesoni clip: tool(http://thegenomefactory.blogspot.com...eads-with.html)
and i got clipped_R1.fq , clipped_R2.fq and clipped_single.fq(orphan reads) files . now i wanna align all these reads to reference sequences and then get FPKM value. so i used bowtie2 :
Code:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} -S [<hit>]
i wrote this:
Code:
bowtie2 -a -X 800 -p 3 -x ~/Desktop/RNA-seq/CD/all_animals_transcription_factors_nt \
{-1 ~/Desktop/RNA-seq/CD/nesoni_clip_clead_reads/clipped_R1.fq -2 ~/Desktop/RNA-seq/CD/nesoni_clip_clead_reads/clipped_R2.fq | -U ~/Desktop/RNA-seq/CD/nesoni_clip_clead_reads/clipped_single.fq} | samtools view -Sb - > hits.bam
but that did not work.
can i do that alignment that paired end and orphan reads at the same time to reference sequences
? if i could, how ? could anyone give me some suggestions?