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Search: Posts Made By: yzzhang
Forum: Bioinformatics 12-29-2019, 09:01 PM
Replies: 2
Views: 1,183
Posted By yzzhang
have you tried CD-hit?

have you tried CD-hit?
Forum: Bioinformatics 04-12-2017, 01:06 PM
Replies: 1
Views: 857
Posted By yzzhang
What is the coverage cutoff? and what is the...

What is the coverage cutoff? and what is the database? I think you can check the parameters used in previous papers and MG-RAST is using
Forum: Bioinformatics 03-08-2017, 05:22 AM
Replies: 21
Views: 7,384
Posted By yzzhang
for our soil samples, the assembled reads...

for our soil samples, the assembled reads normally account for ~50% of the original reads. BTW, our data is >10 Gb per sample.
Forum: Bioinformatics 01-20-2017, 05:18 AM
Replies: 1
Views: 1,264
Posted By yzzhang
fisher exact test maybe fit this.

fisher exact test maybe fit this.
Forum: Bioinformatics 10-20-2016, 04:53 AM
Replies: 1
Views: 1,123
Posted By yzzhang
Several tools such as SPAdes support hybrid...

Several tools such as SPAdes support hybrid assembly using illumina and pacbio reads. Their test suggested illumina reads only generated 92 contigs, while illumina+pacbio generated 5 contigs for E...
Forum: Bioinformatics 07-15-2016, 01:13 PM
Replies: 2
Views: 1,376
Posted By yzzhang
maker-p maybe helps for this purpose....

maker-p maybe helps for this purpose. http://www.ncbi.nlm.nih.gov/pubmed/24306534
Forum: Bioinformatics 06-06-2016, 04:29 AM
Replies: 1
Views: 1,131
Posted By yzzhang
Some tools like Gblocks can do this. However, it...

Some tools like Gblocks can do this. However, it needs all the input alignment files contain same number of sequences and their order should be same. You said the aligned files contain different...
Forum: Bioinformatics 06-03-2016, 06:39 AM
Replies: 4
Views: 2,382
Posted By yzzhang
Previously I tried to use vcftools v0.1.13 to...

Previously I tried to use vcftools v0.1.13 to filter my vcf file with --minGQ option, and it worked fine. So it supposed to be some problem with the vcf file than the software. Have you tried to use...
Forum: Metagenomics 06-01-2016, 04:53 AM
Replies: 2
Views: 2,075
Posted By yzzhang
You can give LSA a try. The paper is here...

You can give LSA a try. The paper is here http://www.nature.com/nbt/journal/v33/n10/full/nbt.3375.html
Forum: Bioinformatics 02-16-2016, 05:01 AM
Replies: 5
Views: 6,119
Posted By yzzhang
I fed SNPhylo only a VCF file and it ran...

I fed SNPhylo only a VCF file and it ran smoothly. If you use SNPhylo, please check the sam headers, it seems SNPhylo only accept number as chromosome header (e.g. >1 but not >chr1) at least for old...
Forum: General 11-18-2015, 04:40 AM
Replies: 9
Views: 2,713
Posted By yzzhang
we did a plant leaf RNA-seq which infected with...

we did a plant leaf RNA-seq which infected with pathogenic bacteria. Around 30 million hiseq pair end reads were generated from each sample, and around 5% of the reads mapped to the bacteria genome...
Forum: Bioinformatics 10-20-2015, 12:54 PM
Replies: 2
Views: 1,226
Posted By yzzhang
which software and parameters you used for gene...

which software and parameters you used for gene prediction? you said "for 13569 contigs of the sequences of", did you mean you blasted the contigs directly against nr database?
Forum: Bioinformatics 10-09-2015, 09:30 AM
Replies: 14
Views: 2,513
Posted By yzzhang
So you used different bam file for cufflinks and...

So you used different bam file for cufflinks and htseqcount? accepted_hits.bam for cufflinks and accepted_hits_sorted_dupRemoved_P1827_101.bam for htseqcount?
Forum: Bioinformatics 07-08-2015, 07:24 AM
Replies: 1
Views: 935
Posted By yzzhang
the Sim4db...

the Sim4db http://www.ncbi.nlm.nih.gov/pubmed/21551146 and Exonerate https://www.ebi.ac.uk/~guy/exonerate/beginner.html work good
Forum: General 05-19-2015, 05:14 AM
Replies: 4
Views: 1,592
Posted By yzzhang
If you want to focus on genes, you can try blast...

If you want to focus on genes, you can try blast methods such as bidirectional best hit, OMCL, etc. several software can do this. I used Get_homologues and it worked well.
Forum: Bioinformatics 03-31-2015, 09:40 AM
Replies: 2
Views: 1,928
Posted By yzzhang
Actually, if you import sam file, you also need...

Actually, if you import sam file, you also need to specify taxonomy file from MEGAN wedsite to get the taxonomy information. As the description "If the BLAST or other comparison files do not contain...
Forum: Metagenomics 03-19-2015, 06:14 AM
Replies: 7
Views: 2,379
Posted By yzzhang
you also can try directly blastx reads against nr...

you also can try directly blastx reads against nr database using diamond, then compare samples using Megan
Forum: Bioinformatics 03-05-2015, 06:57 AM
Replies: 0
Views: 781
Posted By yzzhang
Tigrfam terms to functional categories

Dear all,
I have assigned tigrfam annotations to my genes. Now I want to classify the tigrfam family to higher level functional categories like COG, eggNOG categories. However, I did not find a...
Forum: Illumina/Solexa 02-23-2015, 04:21 AM
Replies: 7
Views: 1,457
Posted By yzzhang
For your assembly, you meant you pulled all data...

For your assembly, you meant you pulled all data together and then assembled using velvet? I think this paper (http://www.nature.com/nature/journal/v514/n7520/abs/nature13786.html) may be a good...
Forum: Metagenomics 01-14-2015, 04:22 AM
Replies: 2
Views: 2,849
Posted By yzzhang
for metagenome functional analysis, you can try...

for metagenome functional analysis, you can try FOAM http://portal.nersc.gov/project/m1317/FOAM/
Forum: General 10-23-2014, 05:18 AM
Replies: 9
Views: 1,371
Posted By yzzhang
you can give the software...

you can give the software abacashttp://abacas.sourceforge.net/ a try
Forum: Bioinformatics 09-30-2014, 11:25 AM
Replies: 3
Views: 1,229
Posted By yzzhang
Based my knowledge, meta_rna is used for...

Based my knowledge, meta_rna is used for extracting rRNA feature from assembled contigs, not from raw reads, right?
Forum: Bioinformatics 09-30-2014, 11:21 AM
Replies: 3
Views: 1,858
Posted By yzzhang
for the question 2, you can upload the...

for the question 2, you can upload the interleaved file. It is acceptable.
Forum: Illumina/Solexa 07-24-2014, 11:54 AM
Replies: 4
Views: 1,520
Posted By yzzhang
for metagenome assembly, is it normal that a...

for metagenome assembly, is it normal that a large percentage of reads can not be assembled to contigs, right?
Forum: Bioinformatics 07-04-2014, 05:19 AM
Replies: 2
Views: 1,186
Posted By yzzhang
abacas may be also...

abacas may be also usefulhttp://abacas.sourceforge.net/Manual.html
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