Xenopus genome files for RNAseq

Question

[rob.costa1234]

I have a clarification of which file to use from Xenbas (laevis). From this link-http://www.xenbase.org/other/static/ftpDatafiles.jsp I think I will use primary gene models (FASTA) file for alignment and gene models (gff3) as GFF3 for annotation. Am I correct? I am doing RNAseq alignment with HISAT.

Here is screen shot of latest genome:

X. laevis v9.1 genome assembly[readme]FASTA Gene Model(s): 1.8.3.2 [readme] primary gene models (gff3) primary gene models (FASTA) gene models (gff3) peptide(FASTA) For the latest versions browse theXenbase FTP site

Answer 1

[Ron]

I would use this file for the X. laevis 9.1 genome https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.xenbase.org_pub_Genomics_JGI_Xenla9.1_Xla.v91.repeatMasked.fa.gz&d=DwMFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=pt2eBGtCyE_Qi6slO5RVtfGA3zOwk4_M88OXcU9-nJI&m=kUg0RuM_AEsQwxgIoPVhP9D4ZMXyRdkA8QAfjwB-YX4&s=u4nOMphkRMUyXQCVUccwn_azLaHwMr2gRQ1J3ms_xeM&e= .

Note, you will have to unzip this as it is a .gz file.

And here is the GFF gene models file.

https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.xenbase.org_pub_Genomics_JGI_Xenla9.1_2016-2D11-2D03_XL9-5F1-5Fv20161019-5FprimaryTranscripts.gff3.gz&d=DwMFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=pt2eBGtCyE_Qi6slO5RVtfGA3zOwk4_M88OXcU9-nJI&m=kUg0RuM_AEsQwxgIoPVhP9D4ZMXyRdkA8QAfjwB-YX4&s=w2RXSey1pXNK5B7DA4wLVKtZ0IwM3j5XMAjyN6lqOHw&e=

[rob.costa1234]

Thanks do you have any suggestion where can I get these files for X tropicalis?

[Ron]

Try checking the links I pasted above.These are xenbase links only.