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Search: Posts Made By: mastal
Forum: Bioinformatics 12-18-2017, 03:35 AM
Replies: 9
Views: 708
Posted By mastal
What does the ~ expand to on your computer? ...

What does the ~ expand to on your computer?

If it's something like /users/kay/ instead of /home/kay/
that might explain why you get the directory/file not found error.
Forum: Bioinformatics 12-17-2017, 02:32 PM
Replies: 9
Views: 708
Posted By mastal
The error message suggests that you have too many...

The error message suggests that you have too many parameters, and trimmomatic is expecting a trimming command at that position, it doesn't really care too much what you call your file. Do you have...
Forum: Bioinformatics 11-13-2017, 02:39 AM
Replies: 6
Views: 524
Posted By mastal
Have you tried running trimmomatic with only the...

Have you tried running trimmomatic with only the ILLUMINACLIP command and not the rest of the quality trimming, just to see how the Illuminaclip part works?

Are you sure you are using the right...
Forum: Bioinformatics 11-12-2017, 03:51 PM
Replies: 6
Views: 524
Posted By mastal
Your command looks OK, why do you think it's not...

Your command looks OK, why do you think it's not working?

Is trimmomatic running, and what output do you get when it finishes?
Forum: Bioinformatics 11-12-2017, 08:25 AM
Replies: 6
Views: 524
Posted By mastal
You have 'PE' in your command, but you appear to...

You have 'PE' in your command, but you appear to be trying to trim SE data, because you are providing the names of one input file and one output file only, so you should change that to 'SE'.
Forum: RNA Sequencing 09-10-2017, 08:59 AM
Replies: 5
Views: 770
Posted By mastal
I haven't used hisat2, but with tophat, not all...

I haven't used hisat2, but with tophat, not all of the stages of the analysis were multi-threaded. So unless you look at top while hisat2 is running one of the multi-threaded stages, you might only...
Forum: Bioinformatics 06-03-2017, 11:46 AM
Replies: 1
Views: 501
Posted By mastal
You don't need to run 'make' if you download the...

You don't need to run 'make' if you download the binary, only if you are trying to build from the source code.

What version of HISAT2 are you using?

I just downloaded the Linux binary for...
Forum: Bioinformatics 05-20-2017, 04:58 AM
Replies: 4
Views: 456
Posted By mastal
I wouldn't worry about the two peaks in the per...

I wouldn't worry about the two peaks in the per sequence quality scores although it looks a bit unusual.

Are the reads all the same length if it is Illumina data, or have they already been trimmed...
Forum: Bioinformatics 05-20-2017, 03:16 AM
Replies: 10
Views: 544
Posted By mastal
You could get a rough estimate, although it could...

You could get a rough estimate, although it could turn out wrong. Use the genome sizes of the most closely related bird species with known genomes as a guide.

You said you had made several...
Forum: Bioinformatics 05-20-2017, 02:56 AM
Replies: 6
Views: 447
Posted By mastal
Yes. that is correct.

Yes. that is correct.
Forum: Bioinformatics 05-19-2017, 10:28 AM
Replies: 6
Views: 447
Posted By mastal
I meant that you should check whether, for genes...

I meant that you should check whether, for genes on the - strand, the exon closest to the rightmost end of the gene is labelled as exon1 or not.

Usually the chromosomal coordinates for a gene are...
Forum: Illumina/Solexa 05-19-2017, 10:20 AM
Replies: 5
Views: 546
Posted By mastal
It's data from the SOLiD platform. They use...

It's data from the SOLiD platform.

They use colorspace rather than basespace,
so you get a sequence of 0,1,2,3 rather than A,T,G,C.

The . indicate missing base calls.
Forum: Bioinformatics 05-19-2017, 07:12 AM
Replies: 10
Views: 544
Posted By mastal
What assembler or assemblers have you used, and...

What assembler or assemblers have you used, and what coverage do you have? For some assemblers too high coverage also leads to problems.
Forum: Bioinformatics 05-19-2017, 06:54 AM
Replies: 6
Views: 447
Posted By mastal
In your gtf file, compare the exon annotations of...

In your gtf file, compare the exon annotations of genes that are on the + strand with those that are on the - strand. The gene you have shown above is on the + strand.
Forum: Bioinformatics 05-19-2017, 06:49 AM
Replies: 10
Views: 544
Posted By mastal
Can you try reference-guided assembly with a...

Can you try reference-guided assembly with a related bird genome?
Forum: Bioinformatics 05-19-2017, 06:19 AM
Replies: 10
Views: 544
Posted By mastal
That actually looks OK, as long as the %GC...

That actually looks OK, as long as the %GC content is what you expect for that genome.
Forum: Bioinformatics 05-19-2017, 05:47 AM
Replies: 10
Views: 544
Posted By mastal
What do the other FastQC plots look like, the per...

What do the other FastQC plots look like, the per base sequence quality, and the per base sequence content?

Have you done any adapter or quality trimming before doing the assembly?
Forum: Bioinformatics 04-29-2017, 03:15 PM
Replies: 188
Views: 52,861
Posted By mastal
Why do you think this indicates failure? You...

Why do you think this indicates failure? You asked trimmomatic to keep both reads of a pair when it finds adapter in palindrome mode, and it appears to have done that.
This does not mean that...
Forum: Bioinformatics 04-29-2017, 02:59 PM
Replies: 188
Views: 52,861
Posted By mastal
Unless you are using a very old version of...

Unless you are using a very old version of trimmomatic, you can use the -basein and -baseout options to specify the prefix of the input and output file names.
Forum: Bioinformatics 04-29-2017, 02:52 PM
Replies: 188
Views: 52,861
Posted By mastal
One point to note might be that the thresholds...

One point to note might be that the thresholds you are using in the ILLUMINACLIP command are 30 for the palindrome mode and 10 for the simple mode, and you are not allowing for any mismatches. So...
Forum: Bioinformatics 04-29-2017, 05:26 AM
Replies: 2
Views: 558
Posted By mastal
Did you check whether any part of the amino acid...

Did you check whether any part of the amino acid sequence corresponds to your nucleotide sequence?

Perhaps blastx translated the entire nucleotide sequence, 1-548, and not just the part annotated...
Forum: Bioinformatics 04-22-2017, 01:42 PM
Replies: 10
Views: 3,207
Posted By mastal
The error message suggests that there is still...

The error message suggests that there is still something not quite right with the syntax.

It looks like you have not added a name for the 2U output file.

I don't think there is anything wrong...
Forum: Bioinformatics 04-22-2017, 12:15 PM
Replies: 10
Views: 3,207
Posted By mastal
More syntax errors. It appears that you...

More syntax errors.

It appears that you only have names for 3 of the 4 output files, you are missing a name for the 2U output file. The command that uses the adapter fasta sequences is...
Forum: Bioinformatics 04-22-2017, 10:20 AM
Replies: 10
Views: 3,207
Posted By mastal
Don't use -basein and -baseout if you give the...

Don't use -basein and -baseout if you give the full names of the input and output files.

You have a typo in the rest of the command, it should be SLIDINGWINDOW not SLINGWINDOW.

You should...
Forum: Illumina/Solexa 04-14-2017, 03:45 PM
Replies: 10
Views: 1,483
Posted By mastal
I think that if you buy only 2 of the kits, you...

I think that if you buy only 2 of the kits, you will get 192 different indexes, not quite enough if you expect to run 240 samples together.
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