I am new to gelaxy. help me with this error
[mem_sam_pe] paired reads have different names: “LH00271:14:22CCGHLT3:4:1101:27028:1080”, “LH00271:14:22CCGHLT3:4:1101:25308:1080”
Welcome, @krupa_natrajan
For an error like yours
The tool is reporting that the two datasets input as a “pair” do not have intact pairs. Sometimes one end of a pair is removed during the quality assurance steps. You can adjust your quality assurance parameter settings to remove these extra singleton reads, or you can remove them after.
This message is from the tool directly, not from Galaxy, so the tool would work the same wherever you ran it with your data. We have another question about this that includes many more details if you are interested: Can use BWA-MEM to concatenated files - #2 by jennaj
What to do
Not all mapping tools will expect intact pairs, and not all settings will trigger that check. But when this comes up, filtering the pairs before mapping is the usual solution. But double check your upstream quality assurance steps to make sure that how it was done is what you wanted to do. Losing one end of a pair can be a valid result!
You can either adjust the settings with your trimming steps. Or, you can use tools like these to correct the pairs after: Fastq interlacer, then Fastq de-interlacer. This removes any “singletons” that are no longer paired after quality assurance.
More about how to interpret fastq data is here → Hands-on: NGS data logistics / NGS data logistics / Introduction to Galaxy Analyses
More about quality assurance and mapping is here → Sequence analysis / Tutorial List
We just completed a training event, and while that is now over, the materials are still published online. Slack help is not available for this, but you can use the GTN chat, and this forum instead. → Galaxy Training Academy 2024
Please give that a try, and if you need more help, you can share more details. How to share your work is in the banner of this forum, or please see here directly.
Hope this helps, but we can certainly follow up more! Please let us know how this works out! 