TopHat BAM file explanation

Question

[qudrat]

When I see TopHat BAM header file it looks like

@SQ SN:chr10    LN:133797422
@SQ SN:chr10_GL383545v1_alt LN:179254
@SQ SN:chr10_GL383546v1_alt LN:309802
@SQ SN:chr10_KI270824v1_alt LN:181496
@SQ SN:chr10_KI270825v1_alt LN:188315

Here i have copied only chr10 header file and it has many lines. What are these multiple line indicates?

[Pierre Lindenbaum]

here is the bam spec: https://github.com/samtools/hts-specs/blob/master/SAMv1.pdf

[qudrat]

Thank you! I have one more question. I am doing Cufflinks analysis on hundreds of index BAM file. Can i do it chromosome wise to save the time as i am interested in only sex chromosome

[Pierre Lindenbaum]

no, you'll get false positives.

[qudrat]

What if I split the BAM file by chromosome using following command samtools view -b input.bam chr1 chr2 chr3 chr4 > output.bam and then Cufflinks is done. How would it produce false positive? Can you help me understand or give me some reference? Actually it has been hampering my work for long and I would be extremely grateful of you.

[Pierre Lindenbaum]

sorry, i was wrong: I thought you wanted to map your reads on each distinct chromosome . I don't know what would happen for cufflink.