YajinMo_Homework_2020/09/28
Task 01
将 THA2.fa map 到 BowtieIndex/YeastGenome 上，得到 THA2.sam; 将 e_coli_500.fq map 到 bowtie-src/indexes/e_coli 上，得到 e_coli_500.sam
将作业文件和比对数据以及其他需要文件拷贝至个人文件夹下：
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$ ls
BowtieIndex e_coli_500_1.sam sam2bed.pl THA2.sam wt1X_thout wt2X_thout
bowtie-src e_coli_500.fq THA2.fa wt1_thout wt2_thout
对THA2.fa进行mapping得到对应.sam文件
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$ bowtie -v 2 -m 10 --best --strata BowtieIndex/YeastGenome -f THA2.fa -S THA2.sam
# reads processed: 1250
# reads with at least one reported alignment: 1158 (92.64%)
# reads that failed to align: 77 (6.16%)
# reads with alignments suppressed due to -m: 15 (1.20%)
Reported 1158 alignments to 1 output stream(s)
同样的，对e_coli_500.fq进行mapping得到对应的.sam文件
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$bowtie -v 1 -m 10 --best --strata bowtie-src/indexes/e_coli -q e_coli_500.fq -S e_coli_500.sam
# reads processed: 500
# reads with at least one reported alignment: 499 (99.80%)
# reads that failed to align: 0 (0.00%)
# reads with alignments suppressed due to -m: 1 (0.20%)
Reported 499 alignments to 1 output stream(s)
Task 02
将上面两个结果均转换为 .bed 文件
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$ perl sam2bed.pl THA2.sam > THA2.bed
$ perl sam2bed.pl e_coli_500.sam > e_coli_500.bed
Task 03
从上一步得到的 THA2.bed 中筛选出一个不含chromosome V 的文件和一个只有chromosome XII 的文件
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$ grep -v $'chrV\t' THA2.bed > THA2_withoutchrV.bed
$ grep $'chrXII\t' THA2.bed > THA2_onlychrXII.bed
$ wc -l THA2_withoutchrV.bed
1125 THA2_withoutchrV.bed
$ wc -l THA2_onlychrXII.bed
169 THA2_onlychrXII.bed