User: wu.zhiqiang.1020
wu.zhiqiang.1020 • 20
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Posts by wu.zhiqiang.1020
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... thanks, I find it and make it go through.
thanks again ...
written 4 months ago by
wu.zhiqiang.1020 • 20
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... 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 months ago by
wu.zhiqiang.1020 • 20
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... 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 ...
written 4 months ago by
wu.zhiqiang.1020 • 20
• updated
4 months ago by
h.mon ♦ 7.2k
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... 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 months ago by
wu.zhiqiang.1020 • 20
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... thanks。 I need to read Trinity again.
...
written 4 months ago by
wu.zhiqiang.1020 • 20
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... it would be helpful to keep the longest isoforms. but I still could not remove the duplicates from other contrig. right?
thanks
...
written 4 months ago by
wu.zhiqiang.1020 • 20
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... yes, I just want to have one longest isoform.
How can I realize that?
ZQ ...
written 4 months ago by
wu.zhiqiang.1020 • 20
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294
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... you mean -c and -t right?
...
written 4 months ago by
wu.zhiqiang.1020 • 20
0
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294
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... 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 ...
written 4 months ago by
wu.zhiqiang.1020 • 20
• updated
4 months ago by
st.ph.n • 990
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... 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 ...
written 5 months ago by
wu.zhiqiang.1020 • 20
• updated
5 months ago by
genomax ♦ 30k
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