User: satshil.r

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satshil.r50
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8 months, 2 weeks ago
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5 years, 10 months ago
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Posts by satshil.r

<prev • 14 results • page 1 of 2 • next >
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Answer: A: Problems with BLAST db, maybe install issue?
... You have to set your blastDB directory in your path. Add where you saved your blastDBs to your bash profile. (~/.bashrc) vim ~/.bashrc #and add the following export BLASTDB="dir_to_blastDB" Or use any gui based editor gedit ~/.bashrc sublime ~/.bashrc ...
written 4.5 years ago by satshil.r50 • updated 5 months ago by RamRS27k
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Answer: A: Deconseq to remove human sequences
... perl deconseq.pl -f myfile_1 -dbs hs_ref_GRCh38_p2 -i 90 -c 90 -out_dir The `-I 90` refers to an identity threshold: > Alignment identity threshold in percentage. The identity is calculated for the part of the query sequence that is aligned to a reference sequence. For example, a query seq ...
written 4.5 years ago by satshil.r50 • updated 5 months ago by RamRS27k
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How stringent/loose should clustering be (CD-HIT-EST/USearch) for multi-kmer assemblies?
... Hello, I have a denovo assembly using a multi-kmer approach (10step range from 21 to 71) on 8 separate samples. I merged the samples and ran cd-hit-est using a 90% identity cutoff. I ran a second instance using a 80% cutoff. However, my assembly still contains 450k contigs. Is it reasonable to cont ...
trinity cd-hit rna-seq velvet sequencing written 4.5 years ago by satshil.r50
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Comment: C: How to merge similar transcripts together?
... It's a multi-kmer approach, so it's technically multiple assemblies combined together. That's why I want to reduce the redundancy. The Assembly is good, ...
written 4.5 years ago by satshil.r50
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How to merge similar transcripts together?
... Hello, I have 8 transcriptomes which I assembled. 4 are from a gonad and 4 are from an ovary. There are also 2 groups within each tissue. I want to create a reference transcriptome containing the contigs from all 8 of my samples, annotate the reference and use it for DGE. I cat'd the 8 files toget ...
fasta assembly rna-seq cd-hit written 4.6 years ago by satshil.r50 • updated 4.6 years ago by Brian Bushnell17k
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Answer: A: STAR crashing due to "FATAL ERROR: Read1 and Read2 are not consistent"
... I just ran L004 by it's self, and it ran perfectly. Ran it again with all 4 reads in one and it crashed with the same error.   Guess I'll just do them individual and merge the sam files together after then... Such a weird error. ...
written 4.9 years ago by satshil.r50
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Comment: C: STAR crashing due to "FATAL ERROR: Read1 and Read2 are not consistent"
... I've already trimmed the data and removed all bad-quality reads as well. ...
written 4.9 years ago by satshil.r50
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Comment: C: STAR crashing due to "FATAL ERROR: Read1 and Read2 are not consistent"
... Just checked all 4 lanes through FastQValidator. Awesome tool, thank you. Fortunately L004 is not corrupt. both reads return ``` fastQValidator --file L004_R2.fq Finished processing L004_R2.fq with 25780124 lines containing 6445031 sequences. There were a total of 0 errors. Returning: 0 : FASTQ_SU ...
written 4.9 years ago by satshil.r50 • updated 7 months ago by RamRS27k
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STAR crashing due to "FATAL ERROR: Read1 and Read2 are not consistent"
... Hello,   I'm trying to use STAR as my aligner, but I get this error: "EXITING because of FATAL ERROR: Read1 and Read2 are not consistent, reached the end of the one before the other one SOLUTION: Check you your input files: they may be corrupted" I checked the logs, and it's my last mate pair, L ...
fastq star dge written 4.9 years ago by satshil.r50
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How to properly map 4 lanes for differential expression using BWA?
... Hey guys, I have 8 samples, each sample having 4 lanes. How do I go about mapping the sample to my reference when there's multiple lanes? I'm not sure how cating the 4 lanes together would work out for counts. Here's my thought process: If I cat the 4 lanes together before mapping (BWA), and then ...
de ht-seq rna-seq bwa differential expression written 4.9 years ago by satshil.r50 • updated 4.9 years ago by Devon Ryan95k

Latest awards to satshil.r

Popular Question 4.5 years ago, created a question with more than 1,000 views. For How to merge similar transcripts together?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For STAR crashing due to "FATAL ERROR: Read1 and Read2 are not consistent"
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How to properly map 4 lanes for differential expression using BWA?
Popular Question 4.5 years ago, created a question with more than 1,000 views. For Process 50k+ sequences with Blastx for Blast2Go

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