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Search: Posts Made By: hugh_hang
Forum: Bioinformatics 01-30-2015, 10:11 PM
Replies: 10
Views: 24,209
Posted By hugh_hang
Unhappy I am afraid I don't know more than you do. I just...

I am afraid I don't know more than you do. I just followed them and get something undesirable.
Forum: Bioinformatics 01-16-2014, 07:33 PM
Replies: 7
Views: 2,320
Posted By hugh_hang
Smile I see, thank you!

I see, thank you!
Forum: Bioinformatics 01-16-2014, 05:52 AM
Replies: 9
Views: 3,495
Posted By hugh_hang
Question do you know if the change will occur in the...

do you know if the change will occur in the newest version in 2014?
Forum: Bioinformatics 01-16-2014, 05:41 AM
Replies: 7
Views: 2,320
Posted By hugh_hang
Question thank you, but what does the '--' means? just...

thank you, but what does the '--' means? just make the bash know the GFF file as stdin?
Forum: Bioinformatics 12-09-2013, 08:38 PM
Replies: 1
Views: 1,395
Posted By hugh_hang
Hello? Does anyone know what happened?

Hello? Does anyone know what happened?
Forum: Bioinformatics 12-04-2013, 07:57 PM
Replies: 1
Views: 1,395
Posted By hugh_hang
Question My repeatmasker(short for RM) seems weird

Hi, I have run RM with cross_match engine and 20 processors. But when I checked the processors I found something strange. When I type

$ ps aux | grep cross_match

I got something like this:
...
Forum: Bioinformatics 09-13-2013, 04:51 AM
Replies: 9
Views: 3,495
Posted By hugh_hang
Thanks, I suddenly realized.

Thanks, I suddenly realized.
Forum: Bioinformatics 09-11-2013, 12:44 AM
Replies: 9
Views: 3,495
Posted By hugh_hang
It is really awesome. I know what to do next,...

It is really awesome. I know what to do next, thanks!
Forum: Bioinformatics 09-10-2013, 08:01 PM
Replies: 9
Views: 3,495
Posted By hugh_hang
I saw '-j' in LTRdigest User’s Manual...

I saw '-j' in LTRdigest User’s Manual (http://www.genometools.org/documents/ltrdigest.pdf) where write:

I thought '-j' is an option of 'gt' command that can be added into all gt tools. Maybe I was...
Forum: Bioinformatics 09-08-2013, 11:32 PM
Replies: 9
Views: 3,495
Posted By hugh_hang
Question genometools parallel

Hi, I am using genometools and find it quite slow with an 1G fasta file.
When running:
$ gt suffixerator ...
It simply used one cpu and was quite slow. Then I tried:
$ gt -j 4 suffixerator ......
Forum: Bioinformatics 08-29-2013, 03:57 AM
Replies: 10
Views: 24,209
Posted By hugh_hang
thank you, could you tell me how to align or map...

thank you, could you tell me how to align or map fastq? what tool will you recommend?
Forum: Bioinformatics 08-29-2013, 12:33 AM
Replies: 10
Views: 24,209
Posted By hugh_hang
Question fastq to bam

Hi!
Can anyone tell me is it possible to convert a .fastq file to a .bam file? How to convert or which tool can I use?
Thanks in advance.
Forum: Bioinformatics 08-22-2013, 04:41 AM
Replies: 3
Views: 5,269
Posted By hugh_hang
if my data is 454 sequencing data from cDNA, is...

if my data is 454 sequencing data from cDNA, is it necessary to generate scaffolds? OR can the scaffolds make any sense?
Forum: Bioinformatics 05-14-2013, 02:02 AM
Replies: 7
Views: 2,320
Posted By hugh_hang
Question problem of LTRdigest in GenomeTools

Hi, I'm a genometools user, I'm here to report a problem (or maybe bug) when I was using ltrdigest on Ubuntu 10.04
I invoked command as follow:
$ gt ltrdigest -aaout yes -hmms ltrhmm/*.hmm test.gff...
Forum: Bioinformatics 04-11-2013, 10:20 PM
Replies: 2
Views: 2,843
Posted By hugh_hang
Thank you! I‘ll pay attention to it.

Thank you! I‘ll pay attention to it.
Forum: Bioinformatics 04-11-2013, 12:02 AM
Replies: 2
Views: 2,843
Posted By hugh_hang
Question Can any softwares or tools convert .KGML files(XML edited) to SVG ones?

In the KEGG website, I've downloaded a KGML file which contains all informations of a pathway. But I want to get the vector graphic of the pathway such as SVG file.
Forum: Bioinformatics 01-24-2013, 10:08 PM
Replies: 18
Views: 4,939
Posted By hugh_hang
I've tried changing format but it doesn't work. I...

I've tried changing format but it doesn't work. I guess we should use TAIR10_pep... for BLAST DBs which is protein files.
Forum: Bioinformatics 01-24-2013, 05:48 AM
Replies: 3
Views: 4,364
Posted By hugh_hang
Does it start to be not free until the beginning...

Does it start to be not free until the beginning of 2013?
Forum: Bioinformatics 01-19-2013, 07:54 AM
Replies: 18
Views: 4,939
Posted By hugh_hang
******************** <BlastOutput_param> ...

********************
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>1e-06</Parameters_expect>
<Parameters_gap-open>11</Parameters_gap-open>...
Forum: Bioinformatics 01-18-2013, 07:16 PM
Replies: 18
Views: 4,939
Posted By hugh_hang
Red face I cleared the unproper tabs(\t) & enters(\r\n)...

I cleared the unproper tabs(\t) & enters(\r\n) and it still doesn't work. I have to doubt if it's because there are too fewer sequences that have found hits or if I should use protain DBs instead of...
Forum: Bioinformatics 01-18-2013, 07:10 PM
Replies: 18
Views: 4,939
Posted By hugh_hang
Thumbs up I see. Thank you.

I see. Thank you.
Forum: Bioinformatics 01-17-2013, 08:09 PM
Replies: 18
Views: 4,939
Posted By hugh_hang
Question Sir, I've done what you recommanded me to do. But...

Sir, I've done what you recommanded me to do. But after I imported the XML file, the mapping and annotation seems not recognise the blast result and give 0 sequences mapped or annotated, my database...
Forum: Bioinformatics 01-17-2013, 06:09 PM
Replies: 18
Views: 4,939
Posted By hugh_hang
Smile My sequences are cDNA-AFLP results, does that...

My sequences are cDNA-AFLP results, does that mean "TAIR10_cdna_..." is a better option? By the way, what does the "pep" in "TAIR10_pep_..." mean?
Forum: Bioinformatics 01-15-2013, 06:59 PM
Replies: 18
Views: 4,939
Posted By hugh_hang
Smile Thank you, I tried clicking "download" in the...

Thank you, I tried clicking "download" in the TAIR website, but I'm really confused by its dendroid file structure.
Forum: Bioinformatics 01-15-2013, 06:12 PM
Replies: 18
Views: 4,939
Posted By hugh_hang
Smile Thank you, I have thought of the option #2, but...

Thank you, I have thought of the option #2, but how can I get the database downloaded from TAIR in the format of .fasta with accession No. like AT4G22340
Showing results 1 to 25 of 28

 


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