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Recent Replies
Comment: SNPs summaries/statistics from output of KisSplice/KisSplice2RefTranscriptome
by
944908620
•
0
I'm unclear how to see the KisSplice2refTranscriptome output .tsv file,. Can you explain the specific meaning of each column? If I have mu…
Comment: Analysis of shRNA/CRISPR screens in 2021
by
dsull
★
2.1k
Also, important to note: although mageck was published a while back, it is still actively maintained (which is important for a tool -- it's…
Answer: Paired-end to Single-end
by
Divon
▴
10
For the sake of completeness, with my Genozip software you could:
```
genozip mydata.bam
genocat mydata.bam.genozip --FLAG +0x40 --out…
Comment: RepeatMasker sequence identifier error
by
Shri hari
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the error states that you need to trim the fasta header.
Comment: No SINEs, LINEs, LTR and DNA elements detected by RepeatMasker
by
Shri hari
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Hey like I said I prepared a denovo repeat library using RepeatModeler, I ran RepeatMasker with the library using the comman`./RepeatMasker…
Comment: Analysis of shRNA/CRISPR screens in 2021
by
dsull
★
2.1k
I've used Mageck for CRISPR screens and it works great.
A few things:
- It, by default, doesn't allow mismatches between read and librar…
Answer: extracting fasta sequence from fasta file with multiple genomes
by
Divon
▴
10
This is trivial to do with Genozip:
```
genozip test.fa
genocat test.fa.genozip -r JQ673480.1 --no-header --sequential | cut -c 10353…
Answer: kissplice2reftranscriptome interpreting output
by
944908620
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I'm unclear how to see the KisSplice2refTranscriptome output .tsv file. Can you explain the specific meaning of each column? If I have mul…
Answer: DESeq2 analysis for multiple conditions
by
195472005
•
0
这个问题还是挺值得回答一下的，我的英文不好，所以再写一个中文版的回答给同胞们看一下：
首先提问中的这种数据输入在新版的 DESeq2 中已经会报错了，因为没有技术重复，结果没有统计学意义。报错信息大概长这样：
```
Error in checkForExperim…
Answer: DESeq2 analysis for multiple conditions
by
195472005
•
0
Deseq2 can return all results between all groups that you input.It seems that your trouhle took place in extract the results with this comm…
Answer: DESeq2 analysis for multiple conditions
by
195472005
•
0
Deseq2 can return all results between all groups that you input.It seems that your trouhle took place in extract the results with this comm…
Comment: How to write a .pdb file using Python
by
Jingtong
•
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Also, could you take a look at my updated version of this question? I want to delete the last two columns and edit the TER line of my outpu…
Comment: Paired-end to Single-end
by
kstangline
▴
30
Hi Kevin,
The last command is below:
> @SQ SN:ERCC-00168 LN:1024 @SQ SN:ERCC-00170 LN:1023 @SQ
> SN:ERCC-00171 LN:505…
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