Where is the output from RepeatMasker saved? I can see the temporary folder in my directory during running but it disappears when it finishes and I can't find a *.masked file anywhere! Is there a separate option to save the output?
-
-
Can you find a file named *.log2?
I advise you to check it and make sure that there is no error message in it. Or can you provide the command line you use?
feixue1039 -
Thanks for your reply - I can't find a *.log2 file either
I ran it as follows: RepeatMasker ../../H99index/H99+mito.fa -lib output_repeats.fa
Then I added the -dir . and some extra output options, -a and -small, to see if that helped, but still nothing. It appears to run fine without throwing any errors, and I can see the files it makes as it runs but when it finishes this all disappearsComment
-
I guess there was never a reply to this problemComment
-
When I run it, it saves the output files to the same directory as the input files are in. So I would guess you have an error along the way.--------------
EthanComment
-
I found it was because I hadn't given the -species option, works fine nowComment
-
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment