Moderator: genomax
genomax ♦ 46k
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Posts by genomax
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Answer:
A: error in star
... You can't use wrong type of file. `/home/administrator/human/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna` is a fasta format sequence file. You need a GTF format file for the `--sjdbGTFfile ` option. ...
written 1 hour ago by
genomax ♦ 46k
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... https://www.biostars.org/p/70167/ ...
written 2 hours ago by
genomax ♦ 46k
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... That option needs to be `--output-dir $oDirectory`. ...
written 4 hours ago by
genomax ♦ 46k
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... https://www.biostars.org/u/6141/ : Agreed. Depending on how savvy OP is they can choose an appropriate method to follow. ...
written 6 hours ago by
genomax ♦ 46k
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Comment:
C: Combine the fastq files
... If what @Devon says is right i.e. `L1_1 `is actually `L001_R1` and `L2_1` is `L002_R1` then you would combine `L1_1` with `L2_1`.
Then `L1_2` with `L2_2`. ...
written 7 hours ago by
genomax ♦ 46k
1
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Answer:
A: install of STAR
... It does appear that `STAR` has been compiled. You would want to add this directory to your `$PATH` to make `STAR` seamlessley available. You can do `export PATH=$PATH:/the_dir_with_STAR`. Otherwise run it as `./STAR -h`. ...
written 7 hours ago by
genomax ♦ 46k
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Comment:
C: Combine the fastq files
... Since these are not `fasta` files based on their names, I edited the title of the post to accurately reflect file type.
Also see: https://www.biostars.org/p/311375/ ...
written 7 hours ago by
genomax ♦ 46k
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Comment:
C: Combine the Fasta Files
... I am not sure why someone chose to change the `R1/R2` nomenclature for read files to `L1/L2` but you can combine R1 files together and R2 files together. You can't do them by clicking on the names in that view you have of some GUI. You will have to do that on the command line by using `cat R1_file ...
written 7 hours ago by
genomax ♦ 46k
1
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Answer:
C: mRNA to protein
... EMBOSS is always a good source for these types of tools. `transeq` (for translation, http://emboss.sourceforge.net/apps/cvs/emboss/apps/transeq.html ) and `getorf` (http://emboss.sourceforge.net/apps/cvs/emboss/apps/getorf.html ) are relevant tools.
There are web based version available if you wan ...
written 8 hours ago by
genomax ♦ 46k
1
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... > 100ish nucleotides to 40kbp
Doing pair wise comparisons does not appear wise in that case. ...
written 9 hours ago by
genomax ♦ 46k
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