gzipped file

[Laurent Manchon]

--hi,


it seems that rsem-calculate-expression can't handle fastq.gz file, don't you ?
is there an option to permit that or i need to uncompress the file before submit it ?

thank you,
Laurent --

[Bo Li]

Hi Laurent,

I guess that bowtie cannot handle fastq.gz file. RSEM calls bowtie to
align reads for it, if bowtie cannot handle, RSEM neither.

The simplest way is to uncompress your file and then run it with RSEM.
Or you can find an aligner that can take .gz file as input. However, in
that case you should be careful about setting parameters for your
aligner. It should output alignments in SAM/BAM format and also generate
as many alignments as it can so that RSEM can decide how to allocate
multireads into each alignment.

Best,
Bo

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[Victor]

Hi Bo,
Can we do gunzip -dc and pipe the output of the fastq.gz to rsem?
I have not tried this yet but something like this?

gunzip -dc $sample | $rsem $alignment_params $ref_path - -S $sample_output
Or maybe write a little wrapper that will do this on the fly?
I'm willing to help out writing a small sub to allow gzip files or
doing something similar to what you do with piping to samtools?
Victor

[b...@cs.wisc.edu]

Hi Victor,

It sounds interesting. However, since RSEM can also accept SAM/BAM
alignment files as input, maybe the best way is ask users to make
alignments by themselves and then provide RSEM an alignment file.

Best,
Bo

[Colin Dewey]

Hi Victor,

With recent versions of BASH, you should be able to do something like:

rsem-calculate-expression --paired-end <(zcat mate1.fastq.gz) <(zcat mate2.fastq.gz) refname samplename

which uses FIFOs

Colin

[Victor]

Did not you could do that. great idea.
I'll give it a try. That way we save some space and processing on
re-zipping files.
Thanks.
Victor