User: Maguelonne

gravatar for Maguelonne
Maguelonne20
Reputation:
20
Status:
New User
Location:
France
Last seen:
3 years, 8 months ago
Joined:
4 years, 6 months ago
Email:
m**************@upmc.fr

Posts by Maguelonne

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Error in sam to bam conversion after bowtie alignment
... you're right! thanks!   ...
written 4.1 years ago by Maguelonne20
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Comment: C: Error in sam to bam conversion after bowtie alignment
... Yes, it doesn't work either. ...
written 4.1 years ago by Maguelonne20
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Error in sam to bam conversion after bowtie alignment
... I used this command line in bowtie: bowtie -v 0 -m 1 ref file1.fastq file2.sam and now I'm trying to convert the sam file I obtained: samtools view -b -S file2.sam > file2.bam and I get this error (even if I specify the -t ref.fa.fai option): [W::sam_read1] parse error at line 1 [main_samv ...
bam samtools sam bowtie written 4.1 years ago by Maguelonne20 • updated 4.1 years ago by thackl2.6k
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Answer: A: Length of miRNA reads after preprocessing steps
... I actually just found an answer: these 50% of reads correspond to phiX contamination! I didn't suspect that because I thought it was "rare" after demultiplexing, but it seems that it's a well known problem.     ...
written 4.6 years ago by Maguelonne20
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Comment: C: Length of miRNA reads after preprocessing steps
... cutadapt  (and adapter sequences which appear as over-expressed sequences in the FastQC results disappear after adapter trimming meaning it went well, right?) ...
written 4.6 years ago by Maguelonne20
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Length of miRNA reads after preprocessing steps
... Hi all, miRNA analysis is new for me. I'm working on reads from a 55 cycle single-read sequencing run and I think I have a problem.. After pre processing steps (removing low quality reads, removing 5' and 3' adapters), 50% of the reads are 55 nucleotides long (that's mean around 1000000 on a total ...
length filtering preprocessing rna-seq mirna seq written 4.6 years ago by Maguelonne20 • updated 3.7 years ago by Biostar ♦♦ 20

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