Chromosome Length Different from Fasta File Used in Genome Generate

[RM]

I am using STAR-2.5.2a.
I used the following command:
/../Tools/STAR-2.5.2a/source/STAR --runMode  genomeGenerate --genomeDir /../Star --genomeFastaFiles /../k.fa

The problem may stem from converting a genbank file to a fasta file using CLC... but I am not sure.
I used the attached fasta file to generate my genome in STAR and I received the following chromosome lengths:
1763312
1727380
1585676
1430218
1395988
1225422
944302
945951
71901
34581
32838
19141
12199

However, according to the input fasta file the chromosome lengths should be:
1734405
1699062
1559681
1406771
1373102
1205333
928821
930443
70722
34014
32299
18827
11999

There are virtually no "N's" in the fasta file sequence. Not sure if I am allowed to post the fasta file publicly here but let me know if you need it.

[Alexander Dobin]

Hi Rob,

sorry for belayed reply.

Did you calculate the "true" chromosome sizes directly from the fasta file you fed STAR?

I would need the fasta file to debug this problem - you could try to reproduce the problem with just one or two chromosomes, and send me the file in a private e-mail dobin @ cshl.edu

Cheers

Alex