I have recently used Bowtie2 to separate out reads mapping to a set of genomes which which works fine however due to the size of my current dataset I had to input as zipped and output as zipped using the command below:
bowtie2 -f --threads 8THREADS -N 1 --un-gz NZ_bowtie_nonaligned_hungate_thread.done --al-gz NZ_bowtie_aligned_hungate_thread.done -x /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed
_trimmed5P_files_.fastq/Hungate1000_index_bowtie -U /ibers/ernie/scratch/thh32/alldata.fa.gz -S /dev/null
The process itself worked fine except for the output zipping. The files themselves were not acknowledged as zipped and so could not be unzipped, however the data inside looked like this:
�95j����q�?�k�6��t��<^L����N� ��m��(N��k9ߟ4�|^��!�\/�߹��M����33���}^�6���۩s�}wsUo/��|.e^6{��\��Sf��sz̋��A���9H�%WLO���u~
Is there anyway to convert this into fasta format again?
Any help would be greatly appreciated.
Many thanks,
Tom
bowtie2 -f --threads 8THREADS -N 1 --un-gz NZ_bowtie_nonaligned_hungate_thread.done --al-gz NZ_bowtie_aligned_hungate_thread.done -x /ibers/ernie/home/thh32/thh32/mcCabe_qualtrimmed
_trimmed5P_files_.fastq/Hungate1000_index_bowtie -U /ibers/ernie/scratch/thh32/alldata.fa.gz -S /dev/null
The process itself worked fine except for the output zipping. The files themselves were not acknowledged as zipped and so could not be unzipped, however the data inside looked like this:
�95j����q�?�k�6��t��<^L����N� ��m��(N��k9ߟ4�|^��!�\/�߹��M����33���}^�6���۩s�}wsUo/��|.e^6{��\��Sf��sz̋��A���9H�%WLO���u~
Is there anyway to convert this into fasta format again?
Any help would be greatly appreciated.
Many thanks,
Tom
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