Daniel:Notebook/GenomeMiner/2013-8-27: Difference between revisions

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'''Replace Matched pairs with Equals'''
'''Replace Matched pairs with Equals'''
  samtools calmd -eS hrcp_sorted_filtered_hl155.sam ../probeseq/Probelist_all.fa > hrcp_sortfilt_eq.sam
  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'''
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_fullindex_samout_p64.out

Revision as of 21:57, 27 August 2013

HL155

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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

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_fullindex_samout_p64.out