EricChu:LabNotesMDA/2015-2-25: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Ericchu
No edit summary
>Ericchu
No edit summary
 
Line 4: Line 4:


~/data_Syn_15T/HL163/BWA$ awk '{print $10}' s_10_1_Indx49_sorted_unmapped.sam > s_10_1_Indx49_sorted_unmapped_blast.txt
~/data_Syn_15T/HL163/BWA$ awk '{print $10}' s_10_1_Indx49_sorted_unmapped.sam > s_10_1_Indx49_sorted_unmapped_blast.txt
/home/kunzhang/softwares/samtools-latest/samtools view s_9_1_Indx53_sorted_unmapped.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > s_9_1_Indx53_sorted_unmapped.fasta

Latest revision as of 00:56, 26 February 2015

~/data_Syn_15T/HL163/BWA$ /home/kunzhang/softwares/samtools-latest/samtools view -b -f 4 s_10_1_Indx49_sorted.bam > s_10_1_Indx49_sorted_unmapped.bam

~/data_Syn_15T/HL163/BWA$ /home/kunzhang/softwares/samtools-latest/samtools view -h s_10_1_Indx49_sorted_unmapped.bam > s_10_1_Indx49_sorted_unmapped.sam

~/data_Syn_15T/HL163/BWA$ awk '{print $10}' s_10_1_Indx49_sorted_unmapped.sam > s_10_1_Indx49_sorted_unmapped_blast.txt

/home/kunzhang/softwares/samtools-latest/samtools view s_9_1_Indx53_sorted_unmapped.bam | awk '{OFS="\t"; print ">"$1"\n"$10}' - > s_9_1_Indx53_sorted_unmapped.fasta