Tools for calculating TPM from BAM files

Question

[309772486]

Hi,

I have a BAM file generated by tophat with genomic coordinates. I am wondering if there is any tool that can be used to generate TPM value for a given set of genes(Bed file input for example)? I tried RSEM, but they seem to only work with BAM file generated with transcripts index. Any help would be appreciated, a header info is as below:

@HD VN:1.0  SO:coordinate
@SQ SN:chr1 LN:249250621
@SQ SN:chr10    LN:135534747
@SQ SN:chr11    LN:135006516
@SQ SN:chr12    LN:133851895
@SQ SN:chr13    LN:115169878
@SQ SN:chr14    LN:107349540
@SQ SN:chr15    LN:102531392
@SQ SN:chr16    LN:90354753
@SQ SN:chr17    LN:81195210
@SQ SN:chr18    LN:78077248
@SQ SN:chr19    LN:59128983
@SQ SN:chr2 LN:243199373
@SQ SN:chr20    LN:63025520
@SQ SN:chr21    LN:48129895
@SQ SN:chr22    LN:51304566
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chrM LN:16571
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@RG ID:Case01   LB:library1 SM:sample1
@PG ID:TopHat   VN:1.3.2*

Answer 1

[Ron]

Try this link .You still need counts:

https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units/