User: juan.crescente

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Posts by juan.crescente

<prev • 68 results • page 1 of 7 • next >
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Comment: C: Removing adaptors from smallRNA seq data
... I should only keep thos 61.7% of reads and then quality trim them? Is there a way to keep only those with trimmomatic? what I'm seeing is that it keeps all the reads ...
written 7 days ago by juan.crescente20
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Comment: C: Removing adaptors from smallRNA seq data
... yes! that part looks good. The problem now is that I still see a huge and only peak in 34nt. I'm expecting to see 21 and 24 peaks (and some more). ...
written 7 days ago by juan.crescente20
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Comment: C: Removing adaptors from smallRNA seq data
... Done, tried it, still getting that weird distribution of reads length where almost all are 34nt. === Summary === Total reads processed: 14,011,412 Reads with adapters: 8,639,554 (61.7%) Reads written (passing filters): 14,011,412 (100.0%) ...
written 9 days ago by juan.crescente20 • updated 8 days ago by genomax68k
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Comment: C: Finding a remote supervisor/mentor/someone to talk to about a possible idea?
... is this more IT or biology related? if it is the first one I might be able to help ...
written 9 days ago by juan.crescente20
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Comment: C: Removing adaptors from smallRNA seq data
... I'm checking this MAS with your feedback. https://mafft.cbrc.jp/alignment/server/spool/_ho.190611011723805E0SZhm924bXDkjdeAHfqVlsfnormal.html what papers are those? in Electronic supplementary material? ...
written 10 days ago by juan.crescente20
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Comment: C: Removing adaptors from smallRNA seq data
... I see tons of over represented sequences, but I do not get hits with adapters anywhere ...
written 10 days ago by juan.crescente20
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Comment: C: Removing adaptors from smallRNA seq data
... Yes, I see nothing with reformat. They do not specify adapters ...
written 10 days ago by juan.crescente20
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Removing adaptors from smallRNA seq data
... Hello! I know this have been asked in many ways before but I've been struggling a while now so it's time to ask. I'm trying to use small RNA seq data from: https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-14-142 These sequences are ~34nt length so they have some kind of adaptor w ...
trimming smallrna adaptor written 10 days ago by juan.crescente20
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Comment: C: Unmapped reads to fastq (hisat2 / samtools / bedtools) not matching pair-end rea
... seems like the output of hisat2 --un-conc is broken. samtools view -b -S data/landic_svevo_1.un.1.sam > data/landic_svevo_1.un.1.bam [W::sam_read1] Parse error at line 2 [main_samview] truncated file. ...
written 9 weeks ago by juan.crescente20
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Comment: C: Unmapped reads to fastq (hisat2 / samtools / bedtools)
... seems like **samtools fastq** only wants bam files, I've updated the question ...
written 9 weeks ago by juan.crescente20

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Popular Question 9 days ago, created a question with more than 1,000 views. For What is a good bioinformatics/biology book for informaticians
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