User: yztxwd

gravatar for yztxwd
yztxwd290
Reputation:
290
Status:
Trusted
Location:
Southern Medical University
Website:
https://yztxwd.github.io/
Last seen:
1 day, 17 hours ago
Joined:
4 months, 2 weeks ago
Email:
y*****@gmail.com

Posts by yztxwd

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Finding distance between a CpG site and a CpG island
... So they built a model to predict the 5mC? Can you provide the link to the article? ...
written 9 weeks ago by yztxwd290
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Comment: C: Transcription Factor motif Enrichment analysis of yeast
... For your first question, do you mean you want to find the TF which regulates your selected genes? You can use the promoter region as the input sequence I don't know what do you refer to on false-positive co-expressed genes ...
written 9 weeks ago by yztxwd290
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Comment: C: Finding distance between a CpG site and a CpG island
... May I ask why do you want to compute this distance? The purpose is important for you to choose the method ...
written 9 weeks ago by yztxwd290
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Comment: C: chip-seq siganl comparision analysis
... The question you asked is about ChIP-seq normalization, it has nothing to do with how many bam files you have. What you should care about is the sequencing depth and the distribution of reads across the genome, there have been many methods proposed to solve this problem, like quantile normalization, ...
written 9 weeks ago by yztxwd290
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Answer: A: Extract sequences from fastA files based on csv chart
... A way by shell command, the idea is first get the ST index for each AX and BX sequence, then concatenate them according to the ST index. test1.fa: >A1 A1SEQUENCE >A2 A2SEQUENCE >A3 A3SEQUENCE test2.fa: >B1 B1SEQUENCE >B2 B2SEQUENCE >B ...
written 10 weeks ago by yztxwd290
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Answer: A: Assign redudancy in pandas dataframe
... Do you mean you want to assign True to all clusters with the same hosts? Try this (Remember to store the dataframe first): def allSame(mylist): return mylist == mylist[::-1] for i in df.index.unique(): df.loc[i, 'Redundant'] = allSame(list(df.loc[i,'Host'])) ...
written 10 weeks ago by yztxwd290
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Comment: C: Help Troubleshooting FASTQC
... And the sequence length distribution error is due to the trimmed sequences won't have the same length as those untrimmed. ...
written 10 weeks ago by yztxwd290
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Comment: C: Process to remove terminal Ns from fasta?
... I misunderstood the question, so remove the terminal N? not ATCG? a quick thought: awk '{if (/>.*/) {print} else { sub(/^N*/, "")sub(/N*$/, ""); print}}' test.fa ...
written 10 weeks ago by yztxwd290
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Answer: A: Process to remove terminal Ns from fasta?
... Use seqkit subseq: example: seqkit subseq -r 6:-1 test.fa # remove the first 5 bases ...
written 10 weeks ago by yztxwd290
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Comment: C: Transcription factor target gene
... For me (I'm not sure it is right), transcription factor target gene refers to those genes with that transcription factor located in regulatory regions responsible for their expression, you can generally call genes with that TF located in the promoter region as target genes ...
written 11 weeks ago by yztxwd290

Latest awards to yztxwd

Rising Star 9 weeks ago, created 50 posts within first three months of joining.
Scholar 10 weeks ago, created an answer that has been accepted. For C: BWA not reporting all similar alignments
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For C: BWA not reporting all similar alignments
Scholar 3 months ago, created an answer that has been accepted. For C: BWA not reporting all similar alignments
Scholar 4 months ago, created an answer that has been accepted. For C: BWA not reporting all similar alignments
Scholar 4 months ago, created an answer that has been accepted. For C: BWA not reporting all similar alignments
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: salmon was only able to assign 0 fragments to transcripts
Teacher 4 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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