read-seqs input parameter improvement about igor HOT 2 OPEN

Hi @penuts7644,
Nope there is no good reason other than: by assuming there are only two colums to the CSV the user cannot make mistakes in the column ordering.
I agree this is not very handy and I will try and make a e change for a slightly more flexible format
Best
Quentin

from igor.

Hi All, @qmarcou @penuts7644

1. Another question. when I input the sequences in fasta format by 'igor -read_seqs' command line, but I did not assign the index for the sample. and I found in the /tmp file, the sequences were automatically added the number with semicolon, e.g. 0; 1; 2; ………………. According to definition, the numbers are the indices, but not the DNA index/barcode. because they are from the same sample, so I really need to assign the index for each sample(all the sequences of each sample)? Anyway, I hope igor can recognize the index by itself if I can input an index file before inputing the sequences. maybe single index or dual indices.
2. If we use the PE sequencing, fast-dump splits, trimmomatic trims. and then we get split read1 and read2 files for each sample. So both of the Read1 and Read2 within one sample should be analyzed, or I just analyze either read1 or read2?
3. Could you please add a plugin or functionality as a translator from DNA into peptide? since TCR chains are special, they need the help of MHC I/II, namely the anchor residues. special amino acids (e.g. Arg, Glu may be different in numbers among different cohorts)

Thanks a million!

from igor.