User: qingxiangg

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qingxiangg40
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Posts by qingxiangg

<prev • 19 results • page 1 of 2 • next >
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Comment: C: BUSCO genome mode giving poor results
... 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 qingxiangg40
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Comment: C: Can I compare the e-value results across different Blast program?
... 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 qingxiangg40
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Can I compare the e-value results across different Blast program?
... 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 ...
blast written 4.3 years ago by qingxiangg40
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Comment: C: Filtering low expression transcripts after a normalized assembly : which fastq f
... 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 qingxiangg40
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Comment: C: Filtering low expression transcripts after a normalized assembly : which fastq f
... 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 qingxiangg40
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Filtering low expression transcripts after a normalized assembly : which fastq file should I used?
... 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 ...
rna-seq written 4.5 years ago by qingxiangg40 • updated 4.4 years ago by Biostar ♦♦ 20
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Comment: C: Scientific Names In Blast Output And Databases
... 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 qingxiangg40
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Comment: C: It should be easy, but...How to keep best hits in blast result when encountering
... Thanks a lot Heriche! I decide to write a script. Thanks! ...
written 4.6 years ago by qingxiangg40
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Answer: A: How to use a fastq file from paired library layout
... 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 qingxiangg40
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It should be easy, but...How to keep best hits in blast result when encountering frame shift?
... 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 ...
blast written 4.6 years ago by qingxiangg40

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