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Recent Replies
Comment: Help aligning Nanopore Long Read RNA seqs
by
rfran010
▴
950
Thanks! I think you might be misinterpreting your coverage output. I believe that just indicates the chromosome and how many reads map to i…
Comment: Empty txt file as an output of "seqkit stats" for multiple fastq files
by
shenwei356
8.5k
Not sure. May be some files are corrupted.
How about try
```
seqkit stats -j 12 *.fastq -T --skip-err -o trimed_count.txt
```
Comment: how linearize nucleotide lines in axt file
by
resug
▴
30
There are two sequences per entry, and the provided awk script has merged the two sequences into a single linear sequence. But the objectiv…
Comment: how linearize nucleotide lines in axt file
by
GenoMax
143k
Using @yokofakun 's [**linearize fasta code**][1]
awk '/^Lm/ {printf("%s%s\t",(N>0?"\n\n":""),$0);N++;next;} {printf("%s",$0);} END …
Comment: Help aligning Nanopore Long Read RNA seqs
by
WouterDeCoster
47k
That is very few reads. Are you sure your run was successful?
Comment: Alignment tool for very short reads (25bp)
by
ATpoint
83k
bowtie aka bowtie1 was developed when these very short reads were state of the art. Id give that a try and see what comes out. Multithreade…
Answer: Alignment tool for very short reads (25bp)
by
Jeremy Leipzig
22k
> What are other reliable tools for the alignment of DNA reads with very short lengths (25-50bp)?
[vmatch][1]
[1]: http://www.vma…
Comment: edgeR batch effect model matrix sanity check
by
kmyers2
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80
Thank you! Appreciate your reply!
Comment: blast Segmentation fault
by
Tina
•
0
I used 'blastn-short', but it still resulted in a segmentation fault. I downloaded the 'nt_euk' index from [NCBI][1].
Thank you.
[1]: h…
Comment: Help aligning Nanopore Long Read RNA seqs
by
sewaw37819
•
0
> What percentage of your library do you expect to be "long-non-coding transcripts"?
A higher percentage than what we are seeing right now…
Comment: Failed to download data from EBI with ascp
by
Michael
54k
Please check my answer. No need to send an email to EBI either.
Answer: Failed to download data from EBI with ascp
by
Michael
54k
**Anonymous Aspera download from ENA works as expected.**
Please follow the official documentation https://ena-docs.readthedocs.io/en/late…
Answer: Alignment tool for very short reads (25bp)
by
Jack Tierney
▴
360
Kudos for writing such a clear and well formatted question. I will give my perspective but don't claim to be an authority. Full disclosure …
Comment: Failed to download data from EBI with ascp
by
ATpoint
83k
Please email EBI and dont post duplicates. Especially not as an answer.
Comment: Help aligning Nanopore Long Read RNA seqs
by
rfran010
▴
950
What percentage of your library do you expect to be "long-non-coding transcripts"?
> (though there IS some coverage, but mostly on whole…
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