我在用bedtools提供的bedtobam功能时遇到了如下问题:
Usage: bedtools bedtobam [OPTIONS] -i <bed/gff/vcf> -g <genome>
其中的genome文件如果直接用NCBI上下载的fna文件比对会报错:
bedToBam -i out2_stand.bed -g GCF_000001405.39_GRCh38.p13_genomic.fna > out2_stand.bam
Less than the req'd two fields were encountered in the genome file (GCF_000001405.39_GRCh38.p13_genomic.fna) at line 1. Exiting.
在网上找相关案例,发现需要的基因组文件是这样的:
$ bedToBam -i rmsk.hg18.chr21.n.bed -g hg18.genome > rmsk.hg18.chr21.bam
但是在网上查找资料发现基本找不到后缀为genome的人类基因组文件,请问在哪里能下载相应文件,或者能用指令将得到的fna格式转化为genome文件吗?
附上bedtobam指令的help:
Tool: bedtools bedtobam (aka bedToBam)
Version: v2.26.0
Summary: Converts feature records to BAM format.
Usage: bedtools bedtobam [OPTIONS] -i <bed/gff/vcf> -g <genome>
Options:
-mapq Set the mappinq quality for the BAM records.
(INT) Default: 255
-bed12 The BED file is in BED12 format. The BAM CIGAR
string will reflect BED "blocks".
-ubam Write uncompressed BAM output. Default writes compressed BAM.
Notes:
(1) BED files must be at least BED4 to create BAM (needs name field).