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3 votes
Accepted

Aligning FASTQs to FASTA reference

Can I expect that after running the command bowtie2 -x ref_index -U seq.fastq.gz -S seq.sam, my seq.sam will only contain the ...
terdon's user avatar
  • 10.2k
3 votes
Accepted

How to know if FASTQ/BAM is from reference genome (FASTA)?

Your post has multiple questions but one of them is not really a question so I'll address everything here: 1. "Some of them could be contaminants, so I'd like to filter them out and get only the ...
Ram RS's user avatar
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3 votes
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ncbi fastq dump error in loop

The main problem is that your script is inadvertently treating a set of file and directory names as a single SRA accession number, all in one variable. You should update it to work with each ...
Jesse's user avatar
  • 947
2 votes
Accepted

Parameter optimisation of minimap2

First of all, use short read option The short read preset (-x sr) for minimap2 is heavily recommended for doing such mapping: ...
Maximilian Press's user avatar
2 votes

Shell script to validate fastq issue

Use the SRR accessions, not the sample-IDs you are using. With entrez e-utils, I found the SRR of GSM2683458: ...
user3479780's user avatar
2 votes

Discrepancy in Read Counts Between FastQ and BAM Files in Adapter-Trimmed Pipeline

"Total number of reads in R1 and R2 FastQ files = mapped and unmapped reads in the corresponding BAM file." there might be confusion regarding the word "read". "record" ...
Yossi Farjoun's user avatar
2 votes

Discrepancy in Read Counts Between FastQ and BAM Files in Adapter-Trimmed Pipeline

My main question is whether you refer to the fastq files after adapter trimming or before. It seems you mean the original fastq files. In that case, any read filtering done by fastp will remove low ...
Maximilian Press's user avatar
2 votes

How to know if FASTQ/BAM is from reference genome (FASTA)?

In general, this answer wouldn't be more correct than @Ram RS' answer but here is how I would approach: I would start everything from scratch, at the end of the day you will most probably need to ...
haci's user avatar
  • 4,162
2 votes

How to split FASTQ reads without re-running `fastq-dump`?

As reads have equal length, so all 152-bp reads can be split into 76-bp read pairs accordingly. We can get Read1 by trimming the tail 76 bp, and get Read2 by trimming the heading 76 bp. No need to re-...
Zhuqiang Zhang's user avatar
1 vote

How to design a synthetic wastewater FASTQ file that could be flagged as "engineered"?

Use existing software to generate simulated fastq files. The input for these tools is generally a set of reference organisms that you'd expect to find in your sample. Simply add your 'engineered' ...
Pallie's user avatar
  • 706
1 vote
Accepted

Downloading multiple SRA files as FASTQ files using SRA Toolkit

That is a classical problem where the folder containing the binary of the tool is not in PATH, see for example https://askubuntu.com/questions/109381/how-to-add-path-of-a-program-to-path-environment-...
ATpoint's user avatar
  • 1,430
1 vote
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Compare FASTQ reconstructions to mtDNA

I will try to answer the different questions. Do you mean aligning the original DNA fragments from a sample to the consensus obtained from the same sample? It makes sense for a few reasons i) ...
Gabriel Renaud's user avatar
1 vote

Fastq file with very high per base sequence quality and no box-whisker plot

Cross-posted and answered on biostars: https://www.biostars.org/p/9583849/#9583850 https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR20708369&display=metadata is a 10x single-...
Ram RS's user avatar
  • 2,425
1 vote

Parameter optimisation of minimap2

Just to follow-up on the performance of minimap2: the solution @MaximillianPress described works. Thousands of hits are obtained for comparatively obscure genes (some will be duplicates). ...
M__'s user avatar
  • 12.6k
1 vote
Accepted

Multiple SRR ID downloaded for single GSM IDs input issue

Basically you're asking why a given GEO accession (GSM...) has many Runs (SRR...). That is because the submitters uploaded multiple fastq files for the same sample, which is the case if a library has ...
ATpoint's user avatar
  • 1,430
1 vote

What are the output files of RNA-Seq from facility?

This cannot be predicted unless you have interacted with them previously. Most commonly a sequencing facility will send raw data as gzipped fastq files, often together with md5 checksums so the user ...
ATpoint's user avatar
  • 1,430
1 vote

How to measure the total size of a fastq file in base pairs?

seqkit stats fastq.gz. Get SeqKit from https://bioinf.shenwei.me/seqkit/usage/
user3479780's user avatar

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