User: User 4014

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User 401430
Reputation:
30
Status:
New User
Location:
Sweden
Last seen:
1 month, 2 weeks ago
Joined:
8 years, 3 months ago
Email:
c**********@ymail.com

Posts by User 4014

<prev • 46 results • page 1 of 5 • next >
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de novo transcriptome assembly with >400K genes. How to proceed?
... Hi folks, I have a de novo transcriptome assembly of a polyploid tree species assembled with K=31 and min length 200 bp. The assembly contains almost 400K genes, and after a reduction with CD-HIT-EST (cut-off=0.97), I have around 350K genes left. Mapping ca. 1/4 of total reads back to the assembly ...
rna-seq written 9 weeks ago by User 401430 • updated 9 weeks ago by Biostar ♦♦ 20
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Choosing a de novo assembly for DGE analysis
... Hi folks, I have two assemblies that are built from k-mer 25 and 31. I ran TrinityStats.pl and busco (eudicot_odb10) to compare them (below). In general k-mer 31 provides better stats, except complete and single buscos that is better with k-mer 25. I prefer k-mer 31, but I am not so sure. May I hav ...
assembly rna-seq written 10 weeks ago by User 401430 • updated 10 weeks ago by konkelzach10
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Comment: C: Problem with FASTA headers and Trinity
... Yes, I used it to add /1 and /2 flags. I have mixed RNA-Seq data, but somehow I managed to remove the flags during rRNA clean-up (with both bowtie2 and bbduk) and binning to separate mixed reads from a plant and a fungus (with STAR). Do you have a suggestion? ...
written 11 weeks ago by User 401430
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Comment: C: Problem with FASTA headers and Trinity
... Actually it is from NovaSeq. The original headers end at #GTGCACCAGGAATCAC, but I guess the 0:N: 00 is added by STAR and /1 is by reformat.sh. ...
written 11 weeks ago by User 401430
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Comment: C: Problem with FASTA headers and Trinity
... Thanks for the link! ...
written 11 weeks ago by User 401430
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Problem with FASTA headers and Trinity
... Hi all, I have a problem with header formats. Since Trinity needs all of the headers to be stitched together, I have some with whitespaces in - that look like this: @A00700:80:HHHNGDRXX:1:2101:30481:11663#GTGCACCAGGAATCAC 0:N: 00 /1 Can anyone help me with some tips on how to fix these with a ba ...
sequence rna-seq written 11 weeks ago by User 401430
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Comment: C: Quality and length trimming for de novo assembly of RNAseq
... Thank you for all your suggestions! I will keep you posted! :) ...
written 3 months ago by User 401430
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Comment: C: Quality and length trimming for de novo assembly of RNAseq
... I glimpsed at some of them and they are mostly on 2 cycles, 2 and 34. The 2nd cycle can be found on both reads, but the 34th cycle ones are on only R2. The remaining bases still have very high quality, though. The facility I used they used NEBNext Ultra II for a while, but they just got NovaSeq. Per ...
written 3 months ago by User 401430
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Comment: C: Quality and length trimming for de novo assembly of RNAseq
... Sorry for getting back to you constantly. May I also have your opinion about "n" bases, please? I have some reads with n bases in my data, which I am surprised that they ain't removed by quality trimming (q20 with bbduk). Is it better to discard those reads? If I remove them, I will lose around 7M f ...
written 3 months ago by User 401430
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Comment: C: Quality and length trimming for de novo assembly of RNAseq
... Thank you very much! I will redo trimming again! :) ...
written 3 months ago by User 401430

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Popular Question 12 weeks ago, created a question with more than 1,000 views. For How To Categorize Transcripts To Subsets Of Go Annotation
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Popular Question 14 months ago, created a question with more than 1,000 views. For quality filtering of Miseq dataset
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