Extracting aligned consensus sequences for every transcript from sam file
Hi,
I am new to RNA seq data anaylsis. I have a RNAseq data which I have aligned against transcriptome using bowtie2.
bowtie2 -x /bowtie2_index Sample.fastq -S Sample1.sam
Is it possible to get the consensus of all aligned sequences for every transcript like this
>transcript_1
actattactctatactcatcatctactactactactactactcaa..
>transcript2
atgctagctagctacgattggatgcagtctatagcgatgtaa....
Kindly help me. Thanks in advance
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What would like to do at the end ? What exactly you want ? Do u just want all the aligned sequences in a fast format or consensus of all the aligned sequences or something else ?
Hi,
I dont want all the aligned seuquences but only the the consensus of all aligned sequence for every transcript.