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Comment: how linearize nucleotide lines in axt file
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resug
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There are two sequences per entry, and the provided awk script has merged the two sequences into a single linear sequence. But the objectiv…
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Using @yokofakun 's [**linearize fasta code**][1]
awk '/^Lm/ {printf("%s%s\t",(N>0?"\n\n":""),$0);N++;next;} {printf("%s",$0);} END …
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That is very few reads. Are you sure your run was successful?
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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…
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> What are other reliable tools for the alignment of DNA reads with very short lengths (25-50bp)?
[vmatch][1]
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Thank you! Appreciate your reply!
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I used 'blastn-short', but it still resulted in a segmentation fault. I downloaded the 'nt_euk' index from NCBI ([enter link description he…
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> What percentage of your library do you expect to be "long-non-coding transcripts"?
A higher percentage than what we are seeing right now…
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Please check my answer. No need to send an email to EBI either.
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**Anonymous Aspera download from ENA works as expected.**
Please follow the official documentation https://ena-docs.readthedocs.io/en/late…
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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 …
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Please email EBI and dont post duplicates. Especially not as an answer.
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What percentage of your library do you expect to be "long-non-coding transcripts"?
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Thank You so much....it was really helpful...i was able to remove the poly G with fastp
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Hi,
Thanks, it was helpul information. I used fastp to remove the poly g and the QC seems to be fine now.
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