All of a sudden a problem with SAM to BAM conversion has cropped up for me.
I used Bowtie 1 to map sRNA reads to a sequence of interested and had a SAM file outputted:
Everything seemed okay at that point, and I wanted to throw the output into IGV to visualize the reads when it yelled at me (rightfully so) that my SAM file was unsorted.
Aha! I thought I would just convert to BAM then sort, then go back to IGV.
So I used this to convert SAM to BAM:
Then I went to sort the file and it finished instantly. I knew something was not right so I looked at my BAM file and it looked like garbled trash (see photo from a related sample).
Any suggestions on what I might have done to screw things up? I have installed nothing/deleted nothing since my SAM to BAM conversions were working well last week.
My previous SAM to BAM converstions were with Tophat output though. Does Bowtie output not do well with a conversion?
I used Bowtie 1 to map sRNA reads to a sequence of interested and had a SAM file outputted:
Code:
@HD VN:1.0 SO:unsorted @SQ SN:centc LN:11067 @PG ID:Bowtie VN:0.12.8 CL:"bowtie -f -S --al /Users/birchlerlab/Desktop/TB9Sb1_centc_aligned.fa /Users/birchlerlab/Desktop/maize_centromeres/centc.fa /Users/birchlerlab/Desktop/TB9SB1_filtered_18_28nt.fa" CTATAAGTCTGTGAAGGTGTCTT 4 * 0 0 * * 0 0 CTATAAGTCTGTGAAGGTGTCTT IIIIIIIIIIIIIIIIIIIIIII XM:i:0 AAGGGGTCGACACAGTTTAGCATG 4 * 0 0 * * 0 0 AAGGGGTCGACACAGTTTAGCATG IIIIIIIIIIIIIIIIIIIIIIII XM:i:0 CCTTCTATCGACGGAGCAGGACGCC 4 * 0 0 * * 0 0 CCTTCTATCGACGGAGCAGGACGCC IIIIIIIIIIIIIIIIIIIIIIIII XM:i:0 CATAACGAAGAAACCCTAGCCT 4 * 0 0 * * 0 0 CATAACGAAGAAACCCTAGCCT IIIIIIIIIIIIIIIIIIIIII XM:i:0 ATGAATGTAGATGAAGGGAACTCA 4 * 0 0 * * 0 0 ATGAATGTAGATGAAGGGAACTCA IIIIIIIIIIIIIIIIIIIIIIII XM:i:0 GAGGATAGCCAAGAGTTCAGGGCC 4 * 0 0 * * 0 0 GAGGATAGCCAAGAGTTCAGGGCC IIIIIIIIIIIIIIIIIIIIIIII XM:i:0 GTGAGTTGAGAATCCATGCGGGCG 4 * 0 0 * * 0 0 GTGAGTTGAGAATCCATGCGGGCG IIIIIIIIIIIIIIIIIIIIIIII XM:i:0 GTGAGTTGAGAATCCATGCGGGCG 4 * 0 0 * * 0 0 GTGAGTTGAGAATCCATGCGGGCG IIIIIIIIIIIIIIIIIIIIIIII XM:i:0 AAGGAGAGTAAGAATTAACAGTGT 4 * 0 0 * * 0 0 AAGGAGAGTAAGAATTAACAGTGT IIIIIIIIIIIIIIIIIIIIIIII XM:i:0 AAGGAGAGTAAGAATTAACAGTGT 4 * 0 0 * * 0 0 AAGGAGAGTAAGAATTAACAGTGT IIIIIIIIIIIIIIIIIIIIIIII XM:i:0
Aha! I thought I would just convert to BAM then sort, then go back to IGV.
So I used this to convert SAM to BAM:
Code:
samtools view -bS ~/TB9SB3.sam > ~/TB9SB3.bam
Any suggestions on what I might have done to screw things up? I have installed nothing/deleted nothing since my SAM to BAM conversions were working well last week.
My previous SAM to BAM converstions were with Tophat output though. Does Bowtie output not do well with a conversion?
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