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Readseq identifying the wrong DATATYPE
Hi there,
Having problems with readseq.jar and not finding an answer anywhere.
Input:
Amino acid .fasta alignments, truncated example:
>ALEXANDRIUM-CATENELLA_TRINITY_DN55193_C0_G1_I1_5
--SVLEQLRSSHEDIENIEKAMS-------K.......SS.......KQT.......VSCEHALKYLIE---N...K...S...KT...A...VEIYQDKDGMRTDDINAL--------Q........GDV
>DINOPHYSIS-ACUMINATA_TRINITY_DN39905_C0_G3_I1_2
---SVLEQLRSAHEDIENIEKAMS-------K.......ST.......RNT.......VACEHSLKYLID...T---K...C...KT...A...VDIYQDKDGMRSDDINAL---
command: Turn .fasta into a .nexus file
`java -jar /PATHs/readseq.jar -f17 EPrGT00050000000311.clean.aln.fa`
`head` of output .nexus file:
#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=23 NCHAR=1007;
FORMAT DATATYPE=DNA INTERLEAVE MISSING=-;
[Name: ALEXANDRIUM-CATENELLA_TRINITY_DN55193_C0_G1_I1_5 Len: 1007 Check: 0]
[Name: DINOPHYSIS-ACUMINATA_TRINITY_DN39905_C0_G3_I1_2 Len: 1007 Check: 0]
Problem: DATATYPE=DNA which should be PROTEIN instead. Previously it would designate the correct datatype.
Problem is occuring on both laptop and cluster.
Questions:
Has this happened to anyone else?
Any idea what may be confusing readseq as to the DATATYPE?
Is it possible to force readseq to set the input as AAs?
Having problems with readseq.jar and not finding an answer anywhere.
Input:
Amino acid .fasta alignments, truncated example:
>ALEXANDRIUM-CATENELLA_TRINITY_DN55193_C0_G1_I1_5
--SVLEQLRSSHEDIENIEKAMS-------K.......SS.......KQT.......VSCEHALKYLIE---N...K...S...KT...A...VEIYQDKDGMRTDDINAL--------Q........GDV
>DINOPHYSIS-ACUMINATA_TRINITY_DN39905_C0_G3_I1_2
---SVLEQLRSAHEDIENIEKAMS-------K.......ST.......RNT.......VACEHSLKYLID...T---K...C...KT...A...VDIYQDKDGMRSDDINAL---
command: Turn .fasta into a .nexus file
`java -jar /PATHs/readseq.jar -f17 EPrGT00050000000311.clean.aln.fa`
`head` of output .nexus file:
#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=23 NCHAR=1007;
FORMAT DATATYPE=DNA INTERLEAVE MISSING=-;
[Name: ALEXANDRIUM-CATENELLA_TRINITY_DN55193_C0_G1_I1_5 Len: 1007 Check: 0]
[Name: DINOPHYSIS-ACUMINATA_TRINITY_DN39905_C0_G3_I1_2 Len: 1007 Check: 0]
Problem: DATATYPE=DNA which should be PROTEIN instead. Previously it would designate the correct datatype.
Problem is occuring on both laptop and cluster.
Questions:
Has this happened to anyone else?
Any idea what may be confusing readseq as to the DATATYPE?
Is it possible to force readseq to set the input as AAs?
