User: qingxiangg
qingxiangg • 40
- Reputation:
- 40
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- New User
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- Last seen:
- 3 years, 10 months ago
- Joined:
- 5 years ago
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Posts by qingxiangg
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... Hi Dear Chris,
It's a long time ago and I'm facing a similar situation.
For transcriptome completeness assessment, the result between BUSCO v 2.0 and CEGMA could be
very different, i.e. BUSCO completness (C:55.1%[S:35.6%,D:19.5%],F:6.3%,M:38.6%,n:978) but cegma produces higher scores (74.19 compl ...
written 4.0 years ago by
qingxiangg • 40
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... Thanks Modha! I've seen that post before and in fact the problem haven't been solved. Thanks anyway! ...
written 4.3 years ago by
qingxiangg • 40
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... Hi everyone,
I'm trying to compare e-values coming from different Blast program exponentially.
I use the same subject database (All-nucl.), only different queries (some are proteins, some are nucl.)
For example, I got e-75 for blastn and e-90 for tblastn for the same subject sequence, then can I ...
written 4.3 years ago by
qingxiangg • 40
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... Hi Atla and Joe thanks for your suggestion
Yes, it's a ALL-FPKM-ZERO problem, I've googled and done troubleshooting these days.
and I think I've got something wrong with the bam file.
I choose the non-normalised data and try to run RSEM-1.2.29 by myself instead of through Trinity.
I didn't reali ...
written 4.5 years ago by
qingxiangg • 40
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... Hi Joe
my non-normalized raw reads: 56597073
normalized raw reads: 7709656 paired reads
I finally choose the raw data to align and quantify according to Atla's suggestion (using perl script in trinity which mapping reads by bowtie, quantifying by RSEM, but still got the ALL FPKM ZERO problem).
I ...
written 4.5 years ago by
qingxiangg • 40
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... Hi all,
I have quite large datasets for transcriptome assembly, so I use --normalize_reads when assembling;
nohup Trinity --seqType fq --left F_clean.fastq --right R_clean.fastq --max_memory 40G --min_contig_length 250 --group_pairs_distance 250 --jaccard_clip --normalize_reads &
Then I ...
written 4.5 years ago by
qingxiangg • 40
• updated
4.4 years ago by
Biostar ♦♦ 20
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... I know this is 14 months ago and I still look at this.. I've got exactly the same problem with you, I download the taxdb.tar.gz and decompressed it to the path of BLASTDB. Then I got N/A in column sscinames. Would you kindly tell me your solution? ...
written 4.6 years ago by
qingxiangg • 40
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... Thanks a lot Heriche! I decide to write a script. Thanks! ...
written 4.6 years ago by
qingxiangg • 40
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... Simple answer to your question,
ERR011088 is the pair file of ERR011087
ERR011090 is the pair file of ERR011089
Check the design description, pair-end files will share the same sample, i.e., Solexa sequencing of MetaHit individual MH0001 random pair end library for ERR011088, ERR011087
...
written 4.6 years ago by
qingxiangg • 40
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... Hello everyone, I'm using Blast+ 2.4.0
This is my question and it bothered me for a while. And this is not duplicate of previous questions like
https://www.biostars.org/p/2864/
https://www.biostars.org/p/111491/
What I want to is to keep best hits in blast result when encountering frame shift
Her ...
written 4.6 years ago by
qingxiangg • 40
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