User: yztxwd

gravatar for yztxwd
yztxwd380
Reputation:
380
Status:
Trusted
Location:
Southern Medical University
Website:
https://yztxwd.github.io/
Last seen:
1 week, 4 days ago
Joined:
8 months, 3 weeks ago
Email:
y*****@gmail.com

Posts by yztxwd

<prev • 70 results • page 1 of 7 • next >
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Answer: A: How to swap the headers between fasta files ?
... parallel --xapply echo ::: $(sed 'n;d' file2.fa) ::: $(sed '1d; n; d' file1.fa) | tr ' ' '\n' ...
written 5 weeks ago by yztxwd380
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Answer: C: Enrichment Analysis for Proteins
... You can try [gprofiler][1], the tutorial can be found on its website [1]: https://biit.cs.ut.ee/gprofiler/gost ...
written 9 weeks ago by yztxwd380
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Comment: C: What if the sequence length distribution differ sharply after I use fastp to tri
... Where is the data from? The length distribution after trimming depends on a lot of things, two example 1st, If the most of your DNA fragments (before ligation) are around 60bp, the sequence reads you get will be original DNA fragment (~60bp) + adapter = 150bp Then trimming will discard the adapt ...
written 9 weeks ago by yztxwd380
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Comment: C: What if the sequence length distribution differ sharply after I use fastp to tri
... First, Per Base Sequence Content represents the proportion of ATCG at each base of the sequences, I don't know why you directly trimming to solve the problem, you should focus on if you have things like adapter contamination or some specific experiment step which will cause this kind of problem. Se ...
written 10 weeks ago by yztxwd380
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Comment: C: How to use Mantel module on jupyter notebook (python)?
... Hi, I think there are two things you can check: 1. Can you import your module in python interactive? means just type python, then import mantel 2. If you can import in pure python, is the python used by jupyter the same as the python in the 1st step? ...
written 10 weeks ago by yztxwd380
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Comment: C: Cutadapt for loop issue
... Yes! I forgot this, it's better to store old IFS, then get it back after things done old_IFS=$IFS IFS=$'\n' for sample in `cat samples.list`; do cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o ${sample}_R1_trimmed.fastq.gz -p ${sample}_R2_trim ...
written 10 weeks ago by yztxwd380
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Comment: C: Cutadapt for loop issue
... The loop processes one sample_RX.fastq.gz a time, so it is obvious that it will process R1 first, then R2 Why don't you just loop over the sample names, like for sample in `cat samples.list`; do cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -o ${samp ...
written 10 weeks ago by yztxwd380
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Comment: C: bedGraphToBigWig Install error
... Emm... Actually I think you can use this command because you are in the bin/ directory of this environment, if you are in another dir it should not work. If you need to use it all the time, you still need to activate the ucsc environment first anyway, cheers! ...
written 10 weeks ago by yztxwd380
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Comment: C: bedGraphToBigWig Install error
... Yes, you have libssl.so.1.1, but you need libssl.so.1.0.0, so try to install openssl version 1.0 to see it can give you a libssl.so.1.0.0 in ~/anaconda2/envs/ucsc/lib I realized the old answer is too complex, you just need to try conda install -n ucsc openssl=1.0 to see if it can fix ...
written 10 weeks ago by yztxwd380
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Comment: C: bedGraphToBigWig Install error
... Okay... Seems strange, it works on my server conda doesn't use the libraries in /lib directory, instead, those files like libxxx.so.x.x lies in the envs/ucsc/lib folder. try conda install -n ucsc openssl=1.0 See if it can work ...
written 10 weeks ago by yztxwd380

Latest awards to yztxwd

Rising Star 6 months ago, created 50 posts within first three months of joining.
Scholar 6 months ago, created an answer that has been accepted. For C: BWA not reporting all similar alignments
Teacher 6 months ago, created an answer with at least 3 up-votes. For C: BWA not reporting all similar alignments
Scholar 7 months ago, created an answer that has been accepted. For C: BWA not reporting all similar alignments
Scholar 8 months ago, created an answer that has been accepted. For C: BWA not reporting all similar alignments
Scholar 8 months ago, created an answer that has been accepted. For C: BWA not reporting all similar alignments
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: salmon was only able to assign 0 fragments to transcripts
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: salmon was only able to assign 0 fragments to transcripts

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