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 &
Replace Matched pairs with Equals
samtools calmd -eS hrcp_sorted_filtered_hl155.sam ../probeseq/Probelist_all.fa > hrcp_sortfilt_eq.sam
So apparently I don't need to use all the indexes. I just used indexes 10-13, which means I can skip everything but those. Using all the indexes might screw up some of the statistics, mostly if someones sequence was close enough to have an alignment (a bad one, most likely).
Phred 64, Shaved Indexing
Bowtie2 with Phred 64 and Fewer Indexes
bowtie2 -x hrcp_probesequences -U s_2_1_Indx12.txt,s_2_1_Indx13.txt,s_3_1_Indx11.txt,s_3_1_Indx10.txt, s_3_1_Indx12.txt,s_2_1_Indx11.txt --phred64 -S hrcp_slimindex_samout_p64.sam