I have a problem with the output from bedtools getfasta, it used to work before. My bed-file looks like this -
C1_64090263 131 164 C1_64090263-1:33 V1_87574936:0 - 33 0
And I am using the command -
bedtools getfasta -fi in.fa -bed file.bed -s -name -fo out.fasta
This reference sequence is 200 bases long. But after extraction I get the sequences as follows
Some invalid characters are formed at the end of sequence, and at the end of the file too many sequences have invalid fasta sequences such as -
There is no problem with the reference fasta as seqtk works on it, but the reverse-strand is also crucial for my sequences.
This happens to most of the sequences on the reverse-strand,some on the plus strand too.
I tried without the name and strandedness options, and also replaced the 5th column with 0, but still it produces no proper fasta files.
Is there a solution to this problem?