User: wu.zhiqiang.1020

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Posts by wu.zhiqiang.1020

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Comment: C: how to extract the longest isoform from trinity outfils
... thanks, I find it and make it go through. thanks again ...
written 4 weeks ago by wu.zhiqiang.102020
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Comment: C: how to extract the longest isoform from trinity outfils
... It need other pm file to load and the same time. I find this link. But I have to search other more pm files also thanks ...
written 4 weeks ago by wu.zhiqiang.102020
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how to extract the longest isoform from trinity outfils
... Dear all, I want to filtered the Trinity outfile for RNAseq assemble. I know this is not the best choice, and there are some scripts online. but they are all not good to use in my data, Could you give me some suggestion on this? my data like this: (Start with > for name) >TRINITY_DN66086_c ...
assembly rna-seq written 4 weeks ago by wu.zhiqiang.102020 • updated 4 weeks ago by h.mon5.3k
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Comment: C: how to use CD_HIT to remove the redundant sequence from trinity output file
... Hi st.ph.n I tried your script, it shown error as Traceback (most recent call last): File "get_longest_iso.py", line 8, in if line.startswith(">"): NameError: name 'line' is not defined could you help me to fix this? I do not know the python. thanks My trinity out start as: >TRI ...
written 4 weeks ago by wu.zhiqiang.102020
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Comment: C: how to use CD_HIT to remove the redundant sequence from trinity output file
... thanks。 I need to read Trinity again. ...
written 4 weeks ago by wu.zhiqiang.102020
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Comment: C: how to use CD_HIT to remove the redundant sequence from trinity output file
... it would be helpful to keep the longest isoforms. but I still could not remove the duplicates from other contrig. right? thanks ...
written 4 weeks ago by wu.zhiqiang.102020
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Comment: C: how to use CD_HIT to remove the redundant sequence from trinity output file
... yes, I just want to have one longest isoform. How can I realize that? ZQ ...
written 4 weeks ago by wu.zhiqiang.102020
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Comment: C: how to use CD_HIT to remove the redundant sequence from trinity output file
... you mean -c and -t right? ...
written 4 weeks ago by wu.zhiqiang.102020
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how to use CD_HIT to remove the redundant sequence from trinity output file
... Dear all, I am trying to use CD-hit to remove the duplicates from the file that is the output from trinity (RNA seq assembly). I used the following parameters: cd-hit-est -i in.fasta -o out_cdhit90.fasta -c 0.90 -n 9 -d 0 -M 0 -T 0 But the output file still contains lots of small or fragmented s ...
assembly rna-seq written 4 weeks ago by wu.zhiqiang.102020 • updated 4 weeks ago by st.ph.n700
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how to use bbnorm to subset the data
... I have a pooled RNA seq data from 5 to 10 individuals at different stages. I want to assemble them and combine all of data as one big fastq files. I use the bbnorm to reduce the replicates. But I have a question about how to set the parameters as: target=100 (tgt) Target normalization ...
assembly bbmap bbnorm rna-seq written 9 weeks ago by wu.zhiqiang.102020 • updated 9 weeks ago by genomax226k

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