Daniel:Notebook/GenomeMiner/2013-8-27
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HL155
Running Bowtie2 with Phred 64
Running bowtie2 again with phred 64 to start the pipeline again. Tried last week but it didn't go so well. I got an error. So I'm running the program again.
Bowtie2 with Phred 64
bowtie2 -x hrcp_probesequences -U s_2_1_Indx12.txt,s_2_1_Indx53.txt,s_2_1_Indx54.txt,s_2_1_Indx04.txt,s_2_1_Indx03.txt,s_2_1_Indx05.txt,s_2_1_Indx02.txt, s_2_1_Indx13.txt,s_2_1_Indx01.txt,s_2_1_Indx55.txt,s_2_1_Indx49.txt,s_3_1_Indx11.txt,s_3_1_Indx10.txt,s_2_1_Indx56.txt, s_2_1_Indx52.txt,s_3_1_Indx12.txt,s_2_1_Indx11.txt,s_2_1_Indx50.txt --phred64 -S hrcp_fullindex_samout_p64.out
Results:
71613792 reads; of these: 71613792 (100.00%) were unpaired; of these: 50674903 (70.76%) aligned 0 times 19321427 (26.98%) aligned exactly 1 time 1617462 (2.26%) aligned >1 times 29.24% overall alignment rate
Sam > Bam and Sort Bam
samtools view -bS hrcp_fullindex_samout_p64.sam | samtools sort - hrcp_sorted_hl155 &
Filter and Convert back to Sam
samtools view -h -F 4 -q 8 hrcp_sorted_hl155.bam > hrcp_sorted_filtered_hl155.sam &