Nr,GenBank, RefSeq, UniProt 数据库的异同
有的文章在做DEG分析时，会把reads比对到RefSeq的转录组上。我也没搞清楚这和直接比对到常规转录组上有什么区别。
文章：Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming
方法：For differential expression analysis, we aligned reads against the refSeq mouse transcriptome using Bowtie version 0.12.7 (Langmead et al., 2009). Expression levels were then stimated using eXpress (Roberts and Pachter, 2013) (version 1.3.0), with gene-level effective counts and RPKM values derived from the sum of the corresponding values for all isoforms of a gene.
refseq 数据库长啥样？
ftp://ftp.ncbi.nlm.nih.gov/refseq/
进到小鼠里：
mRNA_Prot
mRNA_Prot directory
Contents: organisms-specific RefSeq transcript and protein data
{org-name}.files.installed:
reports the md5checksum and files included in the directory
For example: /refseq/H_sapiens/mRNA_Prot/human.files.installed
File Name Conventions:
File name formats are as follows:
common_name.#.molecule_type.format_type
Multiple files may be provided for any given molecule and format type and file
names include a numerical increment. Files with the same numerical increment
are related by content.
For example, the files provided for human are named as:
human.#.rna.fna.gz --fasta report for transcript records
human.#.protein.faa.gz --fasta report for protein records
human.#.rna.gbff.gz --flatfile report for transcript records
human.#.protein.gpff.gz --flatfile report for protein records
下载一个rna.fna文件，里面是这样的：
>NM_001013372.2 Mus musculus neural regeneration protein (Nrp), mRNA CGGTCCAAGGAATTTTTCTGACAAACGCAATAGGCCGACCAGTACTGGAACGCAGTGCGCTTAGCCCCTTTATGGCGGAG GCTGCCATGTTAAAACGGAATGAATCGAAACCCTGGAGTCGTGACCCCGGAAGAACCTGCCAGAGCCGGAATTTCGAGTT CTGCTTCCGGGCCAAACTGTTGGCAGCCTCGAGATGGGGAAGATGGCGGCTGCTGTGGCTTCATTAGCCACGCTGGCTGC AGAGCCCAGAGAGGATGCTTTCCGGAAGCTTTTCCGCTTCTACCGGCAGAGCCGGCCGGGGACAGCGGACCTGGGAGCCG TCATCGACTTCTCAGAGGCGCACTTGGCTCGGAGCCCGAAGCCCGGCGTGCCCCAGGTAGGAAAGGAGGAGTAGTGTGTG CCAGCCTAGCGGCCGACTGGGCCACCCGAGACTGGGCCGCCTCCGGGCCGGCTTTGGAGGGAAGCCCCTGCTGGGCCTGT CCAGTGAGCTGTAATGTCGAGCGATGAGCGACCAGCTGCCTCGCTGTCCCAACGCTCTGGCCACGGCTTGTGCCTTGCCG CCATTTCCCCCAACCCACGCGGGCCACGGCTTGTGCCCTGCCGCCATTTCCCCCAACCCACGCGACCTTGCTAAAAAAAA AAAAAGAAAGAAAAGAAAAGAAAGAAAGAAAGAAAAAAATCTGGAAATTGCTTGTACCTCCTTAACTATCTGTTTAATAC TAATACGATATTTTGTGTAAAGCTCAGAAGAACATCTTCGTGGACGTTAGGGTGGCCTCATAACTTCAGATAAAAGCAGC CATTTAATAAGTCTCAAACCGTTAATCCGTTGGGCCTGAGACTCGATCGACCCTGTCTTCTCTGAGGCTTTGAAAGTAAA GGTAAAATTAGCAGGTTTTTTTCCTGAGAATCTAGGAGCCTGGAGAGATAGCTCAGTAATTAAGAGCATTTACCTACTGG TGTTCCCAAGAACACCAAGTAGATTTGGTTCCTTGCAGCCACGTGGCAGCTCACAGCCTTCTTGTAACTCTTCCGGAGGA TCAGACACCCTCTCTTGAGCTCCACAGGAGAGCACTCGTAGACATGTAAATAAACTTCTAAGCTAAATCTAAACAATTTA TGTACCCTCCCTATTTCTTCGTGATGAGAAGAAAGGGGCCAGAGGGTATG >NR_046233.2 Mus musculus 45S pre-ribosomal RNA (Rn45s), ribosomal RNA ACTGACACGCTGTCCTTTCCCTATTAACACTAAAGGACACTATAAAGAGACCCTTTCGATTTAAGGCTGTTTTGCTTGTC
还是没发现有什么区别！！！
RefSeq转录本是 从gtf得到的转录本的一个子集
后面会再详细展开~